From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!torn!newshub.ccs.yorku.ca!sol.yorku.ca!fs300356 From: fs300356@sol.yorku.ca Newsgroups: bionet.software Subject: Date: 2 Mar 95 01:26:28 -500 Organization: York University Lines: 1 Message-ID: <1995Mar2.012628.1@sol.yorku.ca> NNTP-Posting-Host: sol.yorku.ca From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!torn!newshub.ccs.yorku.ca!sol.yorku.ca!fs300356 From: fs300356@sol.yorku.ca Newsgroups: bionet.software Subject: gaussian Date: 2 Mar 95 00:51:23 -500 Organization: York University Lines: 10 Message-ID: <1995Mar2.005123.1@sol.yorku.ca> NNTP-Posting-Host: sol.yorku.ca Does anyone know a program which can be used to decompose a complicated graph into simple Gaussian graphs or how to do it mathematically? I need it desperately. Please send an email to my account, since I do not read the newsgroup frequently. Thanks. Jinliang LI liangj@biovx1.biology.ucla.edu. From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Shanmugam Ramesh Kumar Newsgroups: bionet.software Subject: SW for tissue culture& hybrid seeds Date: 2 Mar 1995 05:16:31 -0000 Lines: 9 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3j3kbf$obd@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk Hi colleagues: ity areas. sectors. We would appreciate receiving information from the members. shanmugam ramesh kumar From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!umdac!news From: peterl@umdix.umdc.umu.se (Peter Lundberg) Newsgroups: bionet.software Subject: Re: [FOLLOWUP] TIFF Manipulation on a SUN Date: 2 Mar 1995 10:09:29 GMT Organization: Phys Chem, University of Umea, Sweden Lines: 9 Sender: -Not-Authenticated-[2976] Message-ID: <3j45gp$l38@kitten.umu.se> References: NNTP-Posting-Host: plgmac.chem.umu.se X-Posted-From: InterNews 1.0.1@plgmac.chem.umu.se Xdisclaimer: No attempt was made to authenticate the sender's name. Perhaps you could try to use Canvas? There is scaling function there for scaling differently in vertical and horizontal directions. 73, Peter O==O ================================== O==O O==O Peter Lundberg O==O O==O Email: peterl@umdix.umdc.umu.se O==O O==O ============761.91141============= O==O From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: ptaylor@hgmp.mrc.ac.uk (Dr. P.L. Taylor) Newsgroups: bionet.software Subject: GeneJockeyII - problems opening ABI sequencer files Date: 2 Mar 1995 10:18:23 -0000 Lines: 15 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3j461f$6i5@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk I have received a couple of complaints recently from GJII users who are unable to open chromatogram files written by the ABI 373 sequencer. I'm having some difficulty fixing this, since I cannot reproduce the fault on any of the 20 odd machines that I've tried it on. I would really like to know how widespread the problem is. If you are using GeneJockeyII and experiencing this problem please mail me, letting me know what machine and system version you are running. I'll send you an update when I get the bug fixed Phil Taylor | MRC Reproductive Biology Unit | Centre for Reproductive Biology | 37 Chalmers Street mbplt@seqnet.dl.ac.uk | Edinburgh EH3 9EW ptaylor@hgmp.mrc.ac.uk | Scotland. From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!sun1!u735101 From: u735101@sun1.lrz-muenchen.de () Newsgroups: bionet.software Subject: Re: NIH Image for Windows Date: 2 Mar 1995 09:25:49 GMT Organization: Leibniz-Rechenzentrum, Muenchen (Germany) Lines: 7 Distribution: world Message-ID: <3j42ut$5kb@sunserver.lrz-muenchen.de> References: <1995Feb20.165923.730@titan.sfasu.edu> NNTP-Posting-Host: sun1.lrz-muenchen.de >If it exists, does anyone know how and/or where I can get a copy of NIH Image for Windows? Email or >direct post will be much appreciated. Does not exist! It is only available for (Power)Macs. --Harald Felgner From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.nysernet.net!news.sprintlink.net!uunet!pipex!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!msunews!harbinger.cc.monash.edu.au!yarrina.connect.com.au!warrane.connect.com.au!davis.syd.interconnect.com.au!user From: karyn@connect.com.au (Karyn Davis) Newsgroups: bionet.software Subject: Simulation packages? Date: Thu, 02 Mar 1995 18:41:57 +1000 Organization: Connect.com.au P/L, Sydney, Australia Lines: 15 Message-ID: NNTP-Posting-Host: davis.syd.interconnect.com.au Hi, I am looking for a simulation package (like Stella or Simulink) for doing some population modelling. I am specifically interested in packages on the Mac. If anyone out there has used these or other programs, I would be interested in hearing what you think about them. Any information about distributors is also welcomed (especially names of Australian distributors!). Please respond by email to karyn@connect.com.au, as I don't get much time to read news and may miss any replies which are posted. If there is sufficient interest, I will post a summary of replies. Thanks, Karyn Davis From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: Which monitor/card to run X on PC ? Date: 2 Mar 1995 08:09:53 GMT Organization: University of Cambridge, England Lines: 28 Message-ID: <3j3ugh$j7v@lyra.csx.cam.ac.uk> References: <3j1uai$hp3@infoserv.rug.ac.be> <3j2fka$l4u@rc1.vub.ac.be> NNTP-Posting-Host: mole.bio.cam.ac.uk rherzog@ulb.ac.be (Robert Herzog) writes: >kris@bionmr1.bionmr1.rug.ac.be (Kris Boulez) wrote: > we're >>looking for a bigger monitor (17") and a fast graphics card (preferably >>2Mb RAM, VLB). >>I ask this question here because I think some of you might be using >>X-terminals to acces GCG 8.0. >I am very happy with my Philips Brillance 1720 17 in monitor, with a ATI >Graphics Ultra Pro(2mega RAM). I think that the ATI Graphics Xpression is >the today optimal standard. And it cheaper the Ultra Pro. It runs 1280x1024 >with 256 colors, in Linux as well as Windows. I am running XFree86 3.1 with an S3801 ISA card with 2Mb RAM. The VLB version of this (the S3805 chip) is readily available, widely supported (Windows, Linux, and OS/2 Warp all run fine on my machine in 1024x768x65536 and 1280x1024x256). Such cards can probably be had very cheap these days too. A word of warning about the HiColor (65536 colour) modes... the RAMDACs on some S3 cards (including mine) cause a halving of the dot-clock, so that even though it'll do up to 1280x1024x256 non-interlaced, 1024x768x65536 is interlaced. However, under XFree86 3.1, I have found the refresh rate to be adequate, even interlaced. I only have a 14" monitor, so 1280x1024 is a *wee* bit tiny! Tim. From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!torn!newshub.ccs.yorku.ca!sol.yorku.ca!fs300356 From: fs300356@sol.yorku.ca Newsgroups: bionet.software Subject: gaussian Date: 2 Mar 95 01:29:08 -500 Organization: York University Lines: 11 Message-ID: <1995Mar2.012908.1@sol.yorku.ca> NNTP-Posting-Host: sol.yorku.ca Does anyone know a program which can be used to decompose a complicated graph into simple Gaussian graphs or how to do it mathematically? I need it desperately. Please send an email to my account, since I do not read the newsgroup frequently. Thanks. Jinliang LI liangj@biovx1.biology.ucla.edu. From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!rs6000.cmp.ilstu.edu!ajotsuka From: ajotsuka@rs6000.cmp.ilstu.edu (Anthony Otsuka) Subject: Gel Quantitation Software Message-ID: <1995Mar2.154943.50484@rs6000.cmp.ilstu.edu> Date: Thu, 2 Mar 1995 15:49:43 GMT Organization: Illinois State University X-Newsreader: TIN [version 1.2 PL2] Lines: 8 We are planning to purchase image analysis software for our department. If someone could direct me to a FAQ concerning software that can be used to quantitate bands on northern blots or has experience with image analysis programs for IBM PC's or Macs, I would appreciate the help. My guess is that our price range is $200-$2000, but we would consider lower or higher prices depending on features. Thanks, Anthony Otsuka (ajotsuka@rs6000.cmp.ilstu.edu) From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!crick.ssctr.bcm.tmc.edu!rick From: rick@crick.ssctr.bcm.tmc.edu (Richard H. Miller) Newsgroups: bionet.general,bionet.molbio.methds-reagnts,bionet.software Subject: Re: Univ. charging $100/mo./person for mainframe access Date: 2 Mar 1995 15:54:47 GMT Organization: Baylor College of Medicine, Houston, Tx Lines: 59 Distribution: world Message-ID: <3j4po7$2ud@gazette.bcm.tmc.edu> References: <3ilglt$c96@cronkite.ocis.temple.edu> <3j0qqc$8rc@news.doit.wisc.edu> <3j2o89$anb@news.doit.wisc.edu> NNTP-Posting-Host: crick.ssctr.bcm.tmc.edu Xref: biosci bionet.general:13906 bionet.molbio.methds-reagnts:25293 bionet.software:11310 In article <3j2o89$anb@news.doit.wisc.edu>, dalehn@facstaff.wisc.edu (Donald A. Lehn, Ph.D.) writes: |> In article <3j0qqc$8rc@news.doit.wisc.edu>, mtkloth@students.wisc.edu |> says... |> > |> >gold@astro.ocis.temple.edu (Bert Gold) wrote: |> >> |> >> One of the universities where I work has decided to charge $ 100 per |> >> person per month for mainframe access. As everyone in these newsgroups |> >> knows, this kind of access is an absolute requirement for doing |> >> molecular biology in 1995! |> |> You are right. Internet access is a must. If the UW started to charge |> $100.00/month I'd tell them to screw themselves since there are many |> local net providers who will give you unlimited slip access for about |> a third to a quarter of this amount. I thing you misread Mr. Gold said; the charge is $100/month for access to the university's mainframe system. There is nothing said about internet access. If this $100/month represents a flat fee for unlimited access then it may be a bargin (compared to cost recovery where you pay for what you use) 15 years ago when we still did cost recovery for scientific computing, many researchers could easily exceed $100/month in those days when you consider CPU charge, I/O charges and disk storage charges. Since some charge-backs include connect time and memory surcharges I can see the cost could exceed that considerably. In this case, the university should be able to justify the cost structure and, I would hope, be willing to share the model used to develop the charge. (We had no problem in sharing this.) |> |> I would encourage you to drop a note to NIH about this. I bet your |> university is already billing computer access to internet as an |> "overhead" expense for grants it administers. I am willing to bet that |> the govt. wouldn't take kindly to paying for something that isn't |> delivered. And I would encourage you to talk with the people first and see if they can explain the charges and if they are unable/unwilling to explain them, discuss the matter internally first. |> ps. A friend of mine who keeps track of such things estimates that |> the real cost of providing internet services to everyone on the |> net runs less than a $1.00/month (actually more like 50 cents/month). I doubt it, I have done the cost models and unless you have a tremendous user base, there is no way you can do it for $1.00/month (think about it; for say 1200 users you are only talking about $1,200/month and I doubt you can even pay for the hardware and maintenance costs for $1,200/month much less the people costs.) -- Richard H. Miller Email: rick@bcm.tmc.edu Asst. Dir. for Technical Support Voice: (713)798-3532 Baylor College of Medicine US Mail: One Baylor Plaza, 302H Houston, Texas 77030 From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!quagga.ru.ac.za!ucthpx!news From: Ed Rybicki Newsgroups: bionet.software Subject: Re: tree drawing programs for unix machines Date: 2 Mar 1995 14:41:48 GMT Organization: University of Cape Town Lines: 12 Message-ID: <3j4lfc$7qj@ucthpx.uct.ac.za> References: <3j0hv9$6oi@decaxp.harvard.edu> NNTP-Posting-Host: pc24.mic.uct.ac.za eisen@fas.harvard.edu (Michael Eisen) wrote: > I have an old version of the program treetool that does not run on my new > operating system. Does anyone know where I might find new executables (for > and sgi (running irix 5.2) for treetool or where I might find source code? > > Or, does anyone know of an equivalent tree manipulation program for unix > machines? Isn't TREECONW available for UNIX boxes only? I believe so...if so, Des Higgins is the man to contact, and it is in the EMBL software library. From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!uunet!in1.uu.net!newsflash.concordia.ca!news.mcgill.ca!jiminy.Biol.McGill.CA!gpollack From: gpollack@bio1.lan.mcgill.ca (Gerald Pollack) Newsgroups: bionet.software Subject: Re: gaussian Date: Thu, 2 Mar 1995 09:14:06 Organization: McGill University Lines: 26 Message-ID: References: <1995Mar2.012908.1@sol.yorku.ca> NNTP-Posting-Host: jiminy.biol.mcgill.ca X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] In article <1995Mar2.012908.1@sol.yorku.ca> fs300356@sol.yorku.ca writes: >From: fs300356@sol.yorku.ca >Subject: gaussian >Date: 2 Mar 95 01:29:08 -500 >Does anyone know a program which can be used to decompose a complicated >graph into simple Gaussian graphs or how to do it mathematically? I >need it desperately. Please send an email to my account, since I do not >read the newsgroup frequently. >Thanks. >Jinliang LI >liangj@biovx1.biology.ucla.edu. I'm seeking similar information. More specifically, I have data consisting of a frequency distribution of events of different magnitudes, with a number of peaks in the distribution. I suspect that the peaks result from multiples of several unit events, with perhaps 3-4 different unit event amplitudes. I'd like very much to be able to estimate the number of different unit events, and their amplitudes. Please post any advice here, or contact me by email: gpollack@bio1.lan.mcgill.ca Thanks. From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!sunic!news.kth.se!nac.no!nntp.uio.no!usenet From: thomas.hansteen@bio.uio.no (Thomas Hansteen) Newsgroups: bionet.software Subject: Bibliography software Date: 2 Mar 1995 12:47:59 GMT Organization: Universitet i Oslo Lines: 9 Message-ID: <3j4epv$s3a@hermod.uio.no> NNTP-Posting-Host: pcsum39.uio.no X-Newsreader: WinVN version 0.80 We want to collect our litterature databases, who currently are in EndNote-, ProCite- and PopLitt-formats, into one, Word 6.0 (Windows)-compatible Bibliography database. The main qualities we are looking for is import/export routines and friendlyness. Any suggestions? (I have seen above that EndNote for windows, my favorite, is in a prenatal commercial fase, what a pity.) From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!uunet!in1.uu.net!li.net!usenet From: joe mazziliano Newsgroups: bionet.software Subject: Linnaeus Date: 2 Mar 1995 12:40:35 GMT Organization: LI Net (Long Island Network) Lines: 7 Message-ID: <3j4ec3$gen@linet02.li.net> NNTP-Posting-Host: liuser06.li.net does anyone know anything about this program from norway. I have a great need for a taxinomic reference for zooplankton. can anybody help??? tnx From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!umdac!news From: peterl@umdix.umdc.umu.se (Peter Lundberg) Newsgroups: bionet.software Subject: Re: Graph maker for Mac Date: 2 Mar 1995 10:13:46 GMT Organization: Phys Chem, University of Umea, Sweden Lines: 13 Sender: -Not-Authenticated-[2976] Message-ID: <3j45oq$l38@kitten.umu.se> References: NNTP-Posting-Host: plgmac.chem.umu.se X-Posted-From: InterNews 1.0.1@plgmac.chem.umu.se Xdisclaimer: No attempt was made to authenticate the sender's name. In article T.Maemoto@ed.ac.uk (Takuya Maemoto) writes: > Could anybody recommend any graph package with curve fit function for Mac? Try the Share-ware MacCurve Fit. It seems to be good and recommended. 73, Peter O==O ================================== O==O O==O Peter Lundberg O==O O==O Email: peterl@umdix.umdc.umu.se O==O O==O ============761.91141============= O==O From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!elroy.jpl.nasa.gov!netline-fddi.jpl.nasa.gov!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.general,bionet.molbio.methds-reagnts,bionet.software Subject: Re: Univ. charging $100/mo./person for mainframe access Date: 2 Mar 1995 19:32:19 GMT Organization: Biology Division, Caltech, Pasadena, CA USA Lines: 65 Message-ID: <3j56g3$oc6@gap.cco.caltech.edu> References: <3ilglt$c96@cronkite.ocis.temple.edu>,<3j0qqc$8rc@news.doit.wisc.edu> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu Xref: biosci bionet.general:13911 bionet.molbio.methds-reagnts:25310 bionet.software:11315 In article <3j0qqc$8rc@news.doit.wisc.edu>, Michael Kloth writes: >gold@astro.ocis.temple.edu (Bert Gold) wrote: >> >> One of the universities where I work has decided to charge $ 100 per >> person per month for mainframe access. As everyone in these newsgroups >> knows, this kind of access is an absolute requirement for doing >> molecular biology in 1995! > >The University of Wisconsin in Madison not only does not charge This is very misleading. They may not bill for direct usage, but they most definitely are charging someone, somewhere, for this facility. Most likely it is supported by a combination of University overhead charges against research grants and charges against students' tuition. They might also have a direct grant to run it, but that seems kind of unlikely for a central computing facility. Academic computer facility users have an annoying habit of assuming that just because it's easy to click open their inexpensive or free client applications for e-mail, WWW, whatever, that there are no significant costs involved in providing these services. This is grossly incorrect, but the tendency for most central computer facilities to be run off of overhead charges does help to foster this mistaken view. So, here is a short list of what your local computer support people do for you: (The essentials - break any of these and your PC is an island) 1. Purchase, install and maintain the hardware that makes up your local networks. 2. Maintain the logical integrity of your local networks (set up routing, issue network numbers/names, hunt down errant devices, and so forth). 3. Obtain and maintain connection(s) between the local net and the Internet. 4. Purchase, install, and maintain central mail servers and/or timeshare machines. 5. (some sites) Purchase, install, and maintain central file servers. 6. (some sites) Purchase, install, and maintain a firewall between the Internet and your machines. 7. (some sites) Computer hardware/software sales and support at prices lower than general market rates. (Other common computer facility functions - especially with respect to molecular biology users) 8. Purchase, install, and maintain shared hardware. (Generally Unix or VMS machines, but also sometimes PCs and Macs.) 9. Purchase, install, and maintain shared software. For instance, GCG, but also including running servers (WWW,gopher). 10. Consulting services: custom programming, help *understanding* what certain programs do (ie, explaining PHYLIP), prepurchase information for hardware and software.), documentation. I've left a bunch of stuff off and been overly general in others. Note also that a lot of the PC/Mac freeware/shareware was developed by the people who run these sorts of facilities! The bottom line: equipment and services cost real money. Regards, David Mathog mathog@seqvax.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!uunet!in1.uu.net!sunic!trane.uninett.no!nac.no!nntp.uio.no!usenet From: thomas.hansteen@bio.uio.no (Thomas Hansteen) Newsgroups: bionet.software Subject: Re: Linnaeus Date: 2 Mar 1995 19:23:31 GMT Organization: Universitet i Oslo Lines: 13 Message-ID: <3j55vj$3b0@hermod.uio.no> References: <3j4ec3$gen@linet02.li.net> NNTP-Posting-Host: pcsum39.uio.no X-Newsreader: WinVN version 0.80 In article <3j4ec3$gen@linet02.li.net>, joe mazziliano says: > >does anyone know anything about this program from norway. > >I have a great need for a taxinomic reference for zooplankton. > >can anybody help??? > >tnx Try Professor Jahn Trondsen at the University of Oslo. You will find him at: jahn.throndsen@bio.uio.no From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!uunet!in1.uu.net!zib-berlin.de!fu-berlin.de!news.dfn.de!uni-muenster.de!pbio16.uni-muenster.de!user From: tiedtke@vnwz00.uni-muenster.de (Uwe Baumert) Newsgroups: bionet.software Subject: URGENT: help on DeltaSoft's Microplate Analysis on the Mac Date: 2 Mar 1995 12:36:15 GMT Organization: University of Muenster Lines: 25 Message-ID: NNTP-Posting-Host: pbio16.uni-muenster.de Dear netters, we are currently trying to connect an anthos elisa-reader htIII with a mac powerbook 150 (due to lack in spare space) using DeltaSoft II Microplate Analysis Software for the Macintosh. Since the PowerBook has only a seriel printer port we have to use this. But everytime we try to start an analysis via the software we get "Reader doesn't answer" or something like that. When we use the modemport of a Mac Quadra 610 everything works fine. Is there any possibility to get things work? Please answer via private mail. With kind regards, Uwe Baumert -- Uwe Baumert Institute for General Zoology and Genetics University of Muenster Tel.: +49 251 834675 Schlossplatz 5 Fax: +49 251 834723 D-48149 Muenster, Germany e-mail: baumert@uni-muenster.de From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!nntp.msstate.edu!night.primate.wisc.edu!news.doit.wisc.edu!jimmy.buffett.engr.wisc.edu!not-for-mail From: angi@buffett.engr.wisc.edu (Angela Werner) Newsgroups: bionet.general,bionet.molbio.methds-reagnts,bionet.software Subject: Re: Univ. charging $100/mo./person for mainframe access Date: 2 Mar 1995 12:29:48 -0600 Organization: Too much free time Lines: 18 Message-ID: <3j52qt$pl9@jimmy.buffett.engr.wisc.edu> References: <3ilglt$c96@cronkite.ocis.temple.edu> <3j0qqc$8rc@news.doit.wisc.edu> <3j2o89$anb@news.doit.wisc.edu> NNTP-Posting-Host: buffett.engr.wisc.edu Xref: biosci bionet.general:13910 bionet.molbio.methds-reagnts:25308 bionet.software:11312 >>The University of Wisconsin in Madison not only does not charge, but it >>has been encouraging all of the students and faculty to make use of email >>and other internet tools. I think that it has been an enourmous help >>to have these tools available. > > I am a student at UW Madison, and I love the free access. Other than using up valuable study-time, I find it very useful. angi -- -What are we going to do tonight Brain? What we do every night Pinky-- try to take over the world! Pinky and The Brain from The Animaniacs From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!uunet!news.uiowa.edu!uiowa.edu!Paul-pottorff From: Paul-pottorff@uiowa.edu (Paul Pottorff) Newsgroups: bionet.software Subject: NIH Image Date: Thu, 2 Mar 1995 14:38:51 Organization: University of Iowa Lines: 8 Distribution: world Message-ID: NNTP-Posting-Host: 128.255.93.15 Summary: Help Files X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Hey Guys Does anyone know where I can find detailed help documents on NIH Image. I retreived the program from Zippy... but I could not find any detailed help files there. thanks Paul From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!EU.net!Belgium.EU.net!idefix.CS.kuleuven.ac.be!infoserv.rug.ac.be!news From: Frank Schoonjans Newsgroups: bionet.software Subject: Receiver Operating Characteristic Curves Date: 2 Mar 1995 20:10:08 GMT Organization: University of Ghent, Belgium Lines: 5 Message-ID: <3j58n0$1db@infoserv.rug.ac.be> NNTP-Posting-Host: tsv02p04.rug.ac.be The MedCalc statistical program (MS-DOS) now also includes comparison of two receiver operating characteristic curves (derived from the same cases). MedCalc software. fax: +32 9 227 4997. From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!uunet!nih-csl!helix.nih.gov!jip From: jip@helix.nih.gov (John Powell) Subject: Translating from nucleic acid to amino acid. Message-ID: <1995Mar2.211459.17414@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: helix.nih.gov Organization: National Institutes of Health, Bethesda, MD Date: Thu, 2 Mar 1995 21:14:59 GMT Lines: 86 We have placed a modified version of the GDE translate program (for translating from nucleic acid to amino acid) on our anonymous FTP site. The original code has been modified to handle packed fasta formated input files. We also "purified" the code - no known memory leaks. The program processes the input a sequence at a time. We did a 6-frame translation of gbest - all 86K+ sequences in one pass on a SPARC2 with 65M swap space with the following command: zcat gbest.seq.Z |gb2fasta - |translate -tbl 1 -frame 6 - |compress -c > gbest_6f.seq.Z The program is available via anonymous ftp from milo.dcrt.nih.gov (128.231.129.60) under pub/translate as the compressed tar file translate.tar.Z. The man page for the modfied program follows: ------------------------------------------------------------------------------ TRANSLATE(1) USER COMMANDS TRANSLATE(1) NAME translate - translates from nucleic acid to amino acid SYNOPSIS translate [-tbl codon_table] [-frame #] [-min_frame #] [-3] [-gde] [-noc] infile|- translate [-h[elp]] DESCRIPTION Translate program translates the selected sequences from DNA/RNA to Amino Acid. Translate can be used with sequences in either packed FASTA or GDE format. Output is written to standard output. Note that the frame number is appended to the sequence name as ".framenumber". OPTIONS [-tbl codon_table] stop codon table to use: 1 = Universal 2 = Mycoplasma 3 = Yeast 4 = Vert. mito. Default is Universal. [-frame #] Nucleic acide "frame" to translate: 1 = first frame 2 = second frame 3 = third frame 6 = all six frames Defaults to all six frames. [-min_frame #] minimum open reading frame (i.e. shortest amino acid sequence to translate). Default is zero (no minimum). [-3] use triple letter codes. Default is single letter codes. [-gde] input sequence is in GDE format. Default is FASTA format. GDE format with '#' or '%' in the first line is not recognized. [-noc] do not include the sequence description/comments from the first line of sequence in the output. Useful only with FASTA format. infile|- input sequence can be either a packed FASTA sequence file or can be taken from standard input (-) through a pipe, or a GDE format file with -gde switch. Keywords: -- -------- John Powell phone: (301) 496-2963 Building 12A, Room 2033 FAX: (301) 402-2867 National Institutes of Health Bethesda, MD 20892 Internet: jip@helix.nih.gov From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!rutgers!gatech!swrinde!cs.utexas.edu!geraldo.cc.utexas.edu!usenet From: KBowers@access.texas.gov (Kevin L. Bowers) Newsgroups: bionet.software Subject: Need Mol. Wt./Molarity of PCR Primers Software (dos/win) Date: 2 Mar 1995 01:31:22 GMT Organization: The University of Texas at Austin Lines: 8 Message-ID: <3j375a$2fg@geraldo.cc.utexas.edu> Reply-To: KBowers@access.texas.gov NNTP-Posting-Host: slip-7-11.ots.utexas.edu X-Newsreader: WinVN 0.90.4 I am trying to find software for DOS or Windows that will calculate the molecular weight of custom made PCR primers. I have heard that software is available to do this (known as Icon???). Does anyone know of any software capable of doing this? If so where might one obtain this software? Thank You, Kevin L. Bowers From owner-software@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!rutgers!csn!yuma!purdue!haven.umd.edu!hecate.umd.edu!usenet From: bwilliam@oyster.smcm.edu (Bill Williams) Newsgroups: bionet.software Subject: Re: Graph maker for Mac Date: 2 Mar 1995 22:04:29 GMT Organization: St. Mary's College of Maryland Lines: 15 Message-ID: <3j5fdd$42b@umd5.umd.edu> References: NNTP-Posting-Host: williams.smcm.edu X-Posted-From: InterNews 1.0.6@williams.smcm.edu X-Authenticated: bwilliam on POP host oyster.smcm.edu In article T.Maemoto@ed.ac.uk (Takuya Maemoto) writes: > Could anybody recommend any graph package with curve fit function for Mac? Without a doubt: IGOR. Send E-mail to info@wavemetrics.com for information. There is a demo available at their FTP site, but I haven't got the URL handy. _______________________________ Bill Williams bwilliam@oyster.smcm.edu Dept. of Biology St. Mary's College of Maryland St. Mary's City, MD 20686 USA From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!BMMB01.UMESCI.MAINE.EDU!rr From: rr@BMMB01.UMESCI.MAINE.EDU Newsgroups: bionet.software Subject: (none) Date: 2 Mar 1995 12:04:55 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503022304.AA1828@bmmb01.umesci.maine.edu> Reply-To: Robert Roxby Unless it is something you have to do frequently, it is easy to estimate by hand, or if you want to get fancy, with a spreadsheet. No estimate will be better than the pKs you assume for the titratable groups and these are subject to uncertainty. For starters, you could assume the following pKs, which come from measurements by Nozaki and Tanford, which I don't have the exact reference for at hand): alpha-COOH 3.4 D 3.9 E 4.3 H 6.5 alpha-NH3 7.6 C 8.5 (although they could be in SS bonds-you wouldn't know) Y 9.9 K 10.3 R 12.5 Good luck, Bob From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!BMMB01.UMESCI.MAINE.EDU!rr From: rr@BMMB01.UMESCI.MAINE.EDU Newsgroups: bionet.software Subject: RE: Isoelectric points? Date: 2 Mar 1995 12:08:56 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503022308.AA1830@bmmb01.umesci.maine.edu> Reply-To: Robert Roxby Unless it is something you have to do frequently, it is easy to estimate by hand, or if you want to get fancy, with a spreadsheet. No estimate will be better than the pKs you assume for the titratable groups and these are subject to uncertainty. For starters, you could assume the following pKs, which come from measurements by Nozaki and Tanford, which I don't have the exact reference for at hand): alpha-COOH 3.4 D 3.9 E 4.3 H 6.5 alpha-NH3 7.6 C 8.5 (although they could be in SS bonds-you wouldn't know) Y 9.9 K 10.3 R 12.5 Good luck, Bob From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Newsgroups: bionet.software Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!higgins From: higgins@ebi.ac.uk Subject: Re: tree drawing programs for unix machines Sender: news@ebi.ac.uk (Mr news) Message-ID: <1995Mar3.125111@ebi.ac.uk> Date: Fri, 3 Mar 1995 11:51:10 GMT Lines: 23 References: <3j0hv9$6oi@decaxp.harvard.edu> <3j4lfc$7qj@ucthpx.uct.ac.za> Organization: European BioInformatics Institute In article <3j4lfc$7qj@ucthpx.uct.ac.za>, Ed Rybicki writes: > eisen@fas.harvard.edu (Michael Eisen) wrote: >> I have an old version of the program treetool that does not run on my new >> operating system. Does anyone know where I might find new executables (for >> and sgi (running irix 5.2) for treetool or where I might find source code? >> >> Or, does anyone know of an equivalent tree manipulation program for unix >> machines? > > Isn't TREECONW available for UNIX boxes only? I believe so...if so, Des Higgins > is the man to contact, and it is in the EMBL software library. > > No I am not :-). I just had a look and cannot see TREECONW on the EMBL file server. I am interested in tree drawing software though .... When I last looked, TREETOOL was only for Suns .... it is beautiful though. es From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!trane.uninett.no!nntp.uio.no!pcdnr05.uio.no!user From: olam@radium.uio.no (Ola Myklebost) Newsgroups: bionet.software Subject: Re: powerpoint problems Date: Fri, 03 Mar 1995 15:01:42 +0200 Organization: Inst for Cancer Research, Oslo Lines: 16 Message-ID: References: <3iu40r$see@styx.uwa.edu.au> NNTP-Posting-Host: pcdnr05.uio.no In article <3iu40r$see@styx.uwa.edu.au>, mitchell@uniwa.uwa.edu.au (Howard Mitchell) wrote: > we are using the graphics presentation package - > powerpoint. For the most part we have had no problems except that we > cannot get the y axis legend to go vertical. This is a problem with PPT 3.0 which has been corrected in version 4. You may paste in vertical text from another program. -- Ola Myklebost Email ola.myklebost@labmed.uio.no Dept of Tumor Biology Inst for Cancer Research Tel +47-2293-4299 The Norwegian Radium Hospital Fax +47-2252-2421 N-0310 OSLO, Norway From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!quagga.ru.ac.za!nntp.und.ac.za!shrike.und.ac.za!dace From: dace@shrike.und.ac.za (Roy Dace) Newsgroups: bionet.software Subject: Re: WHERE ARE MOLBIO SOFT. SITES FOR PC'S Date: 3 Mar 1995 13:25:35 GMT Organization: University of Natal (Durban), South Africa Lines: 15 Message-ID: <3j75cf$8mi@owl.und.ac.za> References: <1995Feb28.100846.50436@ucl.ac.uk> NNTP-Posting-Host: shrike.und.ac.za X-Newsreader: TIN [version 1.2 PL0] Andrew Martin (martin@bsm.bioc.ucl.ac.uk) wrote: : Run the free Linux Unix clone on your new PC and you'll have access to the : whole world of free Unix software. Have a look at : http://sunsite.unc.edu/mdw/linux.html for information on Linux. Hi, I'm also a Linux user but I'm wondering if you've seen any software of specific interest to molecular biologists available for the OS. I'm specifically looking for a program to help select PCR primers and (for a different project) a port of one which can do cladistic anaylsis. of PCR RAPD's. Thanks, Hal From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!asuvax!news.asu.edu!bdwhaley From: bdwhaley@imap1.asu.edu Newsgroups: bionet.software Subject: Anybody using Labview?(data aquisition/control) Date: 2 Mar 1995 11:11:18 GMT Organization: Arizona State University Lines: 41 Message-ID: <3j494m$8af@news.asu.edu> NNTP-Posting-Host: general2.asu.edu Summary: networking on the net Keywords: automated data aquisition Labview X-Newsreader: TIN [version 1.2 PL2] ::: ::: I'm interested in hearing from people who are familiar with LabVIEW. I am an electrical engineering major at Arizona State University involved in Labview projects. Project Abstracts: 1)Automated data aquisition of a Deep level transient spectroscopy system for detecting impurities in semiconductor material. 2)Control and data logging of an ion beam implanter for making semiconductors. This project involves using a GROUP3 I/O linked by a fiber optic cable. I'm interested in knowing if anyone has written any good drivers for this hardware? 3)Setting up an automated error logging interface at the local Intel plant where they assemble Pentiums chips. This involves linking up several machines to a single PC-interface for extracting error codes for the evaluation of machine performance. These machines come with a SECS interface, anybody familiar with the SEMI SECS protocal? 4)I am getting ready to start on a project at Motorola which involves the upgrading of a "SONA GAUGE" which is used for making a resistivity map of a wafer. Labview is a pure graphics based software. There is no text based code. I am interested in swapping VI's (Virtual instruments) with anyone out there. This summer Intel is sending me to there plants in Malaysia and in the Phillipeans. Any one know of some good sights to see? Let's talk, Brad Whaley my mail: bdwhaley@imap1.asu From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!rutgers!gatech!newsfeed.pitt.edu!hudson.lm.com!netline-fddi.jpl.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.gov!osi-east2.es.net!oracle.pnl.gov!bbs.pnl.gov!gg125 From: pe_keller@pnl.gov (Paul E. Keller) Newsgroups: bionet.software Subject: Annoucement! Biomedical track in the Workshop on Environmental and Energy Applications of Neural Networks Date: 3 Mar 1995 18:40:20 GMT Organization: Battelle - Pacific Northwest Laboratories Lines: 319 Sender: gg125@pnl.gov (Paul E. Keller) Distribution: world Message-ID: <3j7nqk$mkm@bbs.pnl.gov> NNTP-Posting-Host: maddog.pnl.gov Keywords: neural networks, medicine, environment, energy, workshop Originator: gg125@maddog.pnl.gov WORKSHOP ON ENVIRONMENTAL AND ENERGY APPLICATIONS OF NEURAL NETWORKS Pacific Northwest Laboratory Richland, Washington, USA 30-31 March 1995 You'll find the workshop announcement and a list of presentations below. As you can see, there are several biomedical applications. Please forward this message onto those you know who would be interested in attending the workshop. For more information, contact Sherif Hashem (workshop chairman) or myself (Paul Keller) at: Tel: (509) 375-6995 Fax: (509) 375-6631 E-Mail: s_hashem@pnl.gov or pe_keller@pnl.gov Also see the workshop's homepage on the World Wide Web at URL: http://www.emsl.pnl.gov:2080/docs/cie/neural/workshop2/ And FTP directory at: ftp://ftp.pnl.gov/pub/incoming/neural/ (<--- currently) ftp://ftp.pnl.gov/pub/neural/ (<--- after 8 March 1995) ------------------------------------------------------------------------------ The Environmental Molecular Sciences Laboratory (EMSL), Energy Technology Development Initiative, Medical Technology and Systems Initiative, Applied Physics Center, Pacific Northwest Laboratory (PNL); and the Richland Section of the Institute of Electrical and Electronics Engineers (IEEE) are sponsoring a workshop to bring together scientists and engineers interested in investigating environmental and energy applications of artificial neural networks (ANNs). Objectives: ----------- The main objectives of this workshop are: * to provide a forum for presenting and discussing environmental and energy applications of neural networks. * to serve as a means for investigating the potential uses of neural networks in the U.S. Department of Energy's environmental cleanup efforts and energy programs. * to promote collaboration between researchers in national laboratories, academia, and industry to solve real-world problems. Dates: ------ The workshop will be held on 30-31 March 1995 at the Battelle Auditorium, from 8:00 am to 5:00 pm. An introductory tutorial on neural networks will be offered on 29 March 1995, and is recommended for participants who are new to neural networks. ---------------------------------------------------------------------------- LIST OF PRESENTATIONS (Preliminary) *********************************** Biomedical Applications ======================= * The Importance of Artificial Neural Networks in Biomedicine (Invited paper) H.B. Burke, New York Medical College, Valhalla, New York, USA. * (Invited paper). R.L. Watrous, Siemens Corporate Research, Princeton, New Jersey, USA. * Adaptive Logic Networks in Rehabilitation (invited paper). W.W. Armstrong, Dendronic Decisions Ltd and University of Alberta, Edmonton, Alberta, Canada. * Diagnostic System for Detection and Analysis of Auditory Evoked Potentials. Y. Orlov, I.G. Persiantsev, and S.P. Rebrik, A.A. Deviatov, J.S. Shugai, and A.V. Kurganskij, Moscow State University, Moscow, Russia. * Recognizing Patterns in EEG Signals Using Neural Networks Implemented on a Parallel Computer. C.W. Anderson, Colorado State University, Fort Collins, Colorado, USA. * Cardiovascular Modeling and Diagnostics. L.J. Kangas, P.E. Keller, S. Hashem, R.T. Kouzes, Pacific Northwest Laboratory, Richland, Washington, USA, and P.A. Allen, Life Link, Richland, Washington, USA. * Diagnosing Coronary Artery Disease with a Backpropagation Neural Network: Lessons Learned. D.D. Turner, Pacific Northwest Laboratory, Richland, Washington, USA, and E.R. Holmes, III, Sacred Heart Medical Center, Spokane, Washington, USA. * Reduction of a Network of Voltage Gated Conductance Equations to a One-dimensional Map. T. LoFaro, Washington State University, Pullman, Washington, USA. Environmental Applications ========================== * Neural Network Analysis for Hazardous Waste Characterization (invited paper). M. Misra, L.Y. Pratt, C. Farris, and R.O. Hansen, Colorado School of Mines, Golden, Colorado, USA. * A Hybrid Neural Network Structure for Application to Nondestructive TRU Waste Assay. G. Becker, Idaho National Engineering Laboratory, Idaho Falls, Idaho, USA. * Fluorescent Diagnostics of Organic Pollution in Natural Waters: a Neural Network Approach. Y. Orlov, I.G. Persiantsev, and S.P. Rebrik, Moscow State University, Moscow, Russia, and S.M. Babichenko, Institute of Ecology, Estonia. * Reliability and Risk Analysis Using Artificial Neural Networks. D. Robinson, Sandia National Laboratories, Albuquerque, New Mexico, USA. * Neural Networks for Nuclear Spectroscopy. P.E. Keller, L.J. Kangas, G.L. Troyer (*), S. Hashem, and R.T. Kouzes, Pacific Northwest Laboratory, and (*) Westinghouse Hanford Company, Richland, Washington, USA. * Application of Neural Networks to Determine Moisture Content on Humidity- Attenuated NIR Spectra. T. Lopez and B. Philipp, Westinghouse Hanford Company, Richland, Washington, USA. * Artificial Noses and Their Applications. S. Hashem and P.E. Keller, Pacific Northwest Laboratory, Richland, Washington, USA. Environmental/Energy Applications ================================= * Neural Network Models: Insights and Prescriptions from Practical Applications (invited paper). T. Samad, Honeywell Technology Center, Minneapolis, Minnesota, USA. * Application of Computational Neural Networks in Predicting Pollutant Levels due to Fossil-fired Electric Power Generation (invited paper). F. El-Hawary, BH Engineering Systems and Technical University of Nova Scotia, Halifax, Nova Scotia, Canada. * NOx and CO Prediction in Fossil Fuel Plants by Neural Networks. T. Adali and B. Bakal, University of Maryland Baltimore County, Baltimore, Maryland, USA. Energy Applications =================== * Twin Signal Signature Sensing: Application to Shorted Winding Monitoring, Detection and Localization (invited paper). R.J. Marks II, M.A. El-Sharkawi, R.J. Streifel, and I. Kerszenbaum, University of Washington, Seattle, Washington, USA. * Investigation of Neural-Net Based Control Strategies for Improved Power System Dynamic Performance (invited paper). D. Sobajic, Electric Power Research Institute, Palo Alto, California, USA. * Feasibility of using Adaptive Logic Networks to Predict Compressor Unit Failure. W.W. Armstrong, Dendronic Decisions Ltd and University of Alberta, Edmonton, Alberta, Canada. * Near and Long-Term Load Prediction Using Radial Basis Function Networks. M.F. Hancock, CSI Corporation and Rollins College, Melborne, Florida, USA. * Design of a Hybrid Wind Power Storage and Generation System for a Remote Community. S.S. Devgan and D.R. Walker, Jr., Tennessee State University, Nashville, Tennessee, USA. * The Hybrid-paradigm Conception of Ongoing or Outlined Sequel Projects to FUELCON: A Concentric Attack on the Nuclear-fuel On-line Management Problem. A. Galperin, E. Nissan (*), and H. Siegelmann, Ben-Gurion University, Beer-Sheva, Israel, and (*) The University of Greenwich, London, United Kingdom. * Reinforcement Learning for Control: How to Decrease Learning Time. C.W. Anderson, Colorado State University, Fort Collins, Colorado, USA. * Distribution Short-Term Load Forecasting. R.C. Stratton and K.L. Gaustad, Pacific Northwest Laboratory, Richland, Washington, USA. Commercial Applications ======================= * Estimating Dollar-value Outcomes of Workman's Compensation Claims Using Radial Basis Function Networks. M.F. Hancock, CSI Corporation and Rollins College, Melborne, Florida, USA. * Stochastic Modelling Hints for Neural Network Prediction. R. Drossu and Z. Obradovic, Washington State University, Pullman, Washington, USA. For More Information, Contact: ------------------------------ Dr. Sherif Hashem Pacific Northwest Laboratory P.O. Box 999, M/S K1-87 Richland, WA 99352, USA Telephone: 509-375-6995 Fax.: 509-375-6631 Internet: s_hashem@pnl.gov World Wide Web URL: http://www.emsl.pnl.gov:2080/people/bionames/hashem_s.html Also see the workshop's homepage on the World Wide Web at URL: http://www.emsl.pnl.gov:2080/docs/cie/neural/workshop2/homepage.html ============================================================================ Registration: ------------- The registration fee is $120 ($75 for students and postdoctoral fellows). Early registration by 15 March 1995, is $100 ($50 for students and postdoctoral fellows). ____________________________________________________________________________ REGISTRATION FORM Name: _______________________________________________ Title: _______________________________________________ Affiliation: _______________________________________________ _______________________________________________ Address: _______________________________________________ _______________________________________________ _______________________________________________ _______________________________________________ Telephone: _______________________________________________ Fax: _______________________________________________ E-mail: _______________________________________________ WWW: _______________________________________________ [ ] I am interested in attending the neural network tutorial (no additional fee is required). Registration Fee: ----------------- Regular: $100 ($120 after 15 March 1995). Student and Postdocs: $50 ($75 after 15 March 1995). Please make your check payable to Battelle (in US funds). Mail the completed form and check to: Janice Gunter WEEANN Registration Pacific Northwest Laboratory P.O. Box 999, M/S K1-87 Richland, WA 99352, USA ***************************************************************************** The Pacific Northwest Laboratory (PNL) is a multiprogram national laboratory operated for the U.S. Department of Energy by the Battelle Memorial Institute. To provide the basic research needed to meet environmental cleanup, the Environmental Sciences Laboratory (EMSL) is being constructed at PNL. The prime mission of the EMSL and its associated research programs is to advance scientific knowledge in support of the long-term mission of the U.S. Department of Energy in environmental restoration and waste management. ***************************************************************************** For More Information, Contact: ------------------------------ Dr. Sherif Hashem Pacific Northwest Laboratory P.O. Box 999, M/S K1-87 Richland, WA 99352, USA Telephone: 509-375-6995 Fax.: 509-375-6631 Internet: s_hashem@pnl.gov World Wide Web URL: http://www.emsl.pnl.gov:2080/people/bionames/hashem_s.html Also see the workshop's homepage on the World Wide Web at URL: http://www.emsl.pnl.gov:2080/docs/cie/neural/workshop2/homepage.html And FTP directory at: ftp://ftp.pnl.gov/pub/incoming/neural/ (<--- currently) ftp://ftp.pnl.gov/pub/neural/ (<--- after 8 March 1995) ============================================================================ Registration: ------------- The registration fee is $120 ($75 for students and postdoctoral fellows). Early registration by 15 March 1995, is $100 ($50 for students and postdoctoral fellows). ____________________________________________________________________________ REGISTRATION FORM Name: _______________________________________________ Title: _______________________________________________ Affiliation: _______________________________________________ _______________________________________________ Address: _______________________________________________ _______________________________________________ _______________________________________________ _______________________________________________ Telephone: _______________________________________________ Fax: _______________________________________________ E-mail: _______________________________________________ WWW: _______________________________________________ [ ] I am interested in attending the neural network tutorial (no additional fee is required). [ ] I am interested in a bus tour of the Hanford Site (a Department of Energy site located north of Richland, Washington). Registration Fee: ----------------- Regular: $100 ($120 after 15 March 1995). Student and Postdocs: $50 ($75 after 15 March 1995). Please make your check payable to Battelle (in US funds). Mail the completed form and check to: Janice Gunter WEEANN Registration Pacific Northwest Laboratory P.O. Box 999, M/S K1-87 Richland, WA 99352, USA ***************************************************************************** The Pacific Northwest Laboratory (PNL) is a multiprogram national laboratory operated for the U.S. Department of Energy by the Battelle Memorial Institute. To provide the basic research needed to meet environmental cleanup, the Environmental Sciences Laboratory (EMSL) is being constructed at PNL. The prime mission of the EMSL and its associated research programs is to advance scientific knowledge in support of the long-term mission of the U.S. Department of Energy in environmental restoration and waste management. ***************************************************************************** -- _____________________.______________________________._____________________. Paul E. Keller, Ph.D | Pacific Northwest Laboratory | pe_keller@pnl.gov | Research Scientist | P.O. Box 999, M/S K1-87 | Tel: (509) 375-2254 | | Richland, WA 99352, USA | Fax: (509) 375-6631 | From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!rutgers!gatech!swrinde!cs.utexas.edu!news.sprintlink.net!uunet!in1.uu.net!news.claremont.edu!paris.ics.uci.edu!news.service.uci.edu!buggus.mmg.uci.edu!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: New WAIS dbs: comp.sy.sgi, info-mac, comp.os.linux Date: Fri, 03 Mar 1995 10:15:58 -0800 Organization: Microbiology and Molecular Genetics, UC Irvine Lines: 115 Message-ID: NNTP-Posting-Host: buggus.mmg.uci.edu Hi All, While this is not strictly bio-related, these services were set up by myself for that audience here at UCI and elsewhere, so you may as well benefit from them. Especially with Linux taking off in biology labs as an alternative to the more expensive unices, this database may be of assistance to people trying to get up and running with the system. (It's a little 486/Linux box hosting the info-mac and linux dbs). The entire comp.sys.sgi hierarchy (about 190MB - thanks to SGI for the hosting disk) is available via the individual groups, updated twice a week automatically: comp.sys.sgi.admin comp.sys.sgi.announce comp.sys.sgi.apps comp.sys.sgi.audio comp.sys.sgi.bugs comp.sys.sgi.graphics comp.sys.sgi.hardware comp.sys.sgi.misc comp.sys.mips URL: wais://hornet.mmg.uci.edu/comp.sys.sgi.[group]?query boolean query ... ie wais://hornet.mmg.uci.edu/comp.sys.sgi.apps?image and processing and free -------------------------------------------------------------------------- The info-mac electronic periodical which is useful for the announcements of free-, share-, and comm-ware as well as updates, fixes, and FAQs, reformatted slightly is available as: info-mac Volumes 10 thru 12 inclusive (~30MB) info-mac95 Volume 13 (1995), updated about weekly (haven't finished automating it yet) URL: wais://ih34.hsis.uci.edu/info-mac?query boolean query ... wais://ih34.hsis.uci.edu/info-mac95?query boolean query ... ie: wais://ih34.hsis.uci.edu/info-mac?molecular and biology or DNA -------------------------------------------------------------------------- Most of the comp.os.linux hierarchy, starting from a couple weeks ago, is also available, re-indexed nightly comp.os.linux.admin comp.os.linux.announce comp.os.linux.hardware comp.os.linux.help comp.os.linux.misc comp.os.linux.networking comp.os.linux.x This feed rate is about 0.5 MB/day, so eventually I'll have to start rolling it over (or get another disk). URL: wais://ih34.hsis.uci.edu/linux?query boolean query ... ie: wais://ih34.hsis.uci.edu/linux?scsi and adaptec and eisa -------------------------------------------------------------------------- You can get to all these databases and more via either my home page: http://hornet.mmg.uci.edu/~hjm/hjm.html or via the SGI database page: http://hornet.mmg.uci.edu/~hjm/projects/sgi.wais.html Web/Net Clients: Mosaic (wais support builtin for X windows version 2.4 and later) Netscape (wais support NOT builtin - have to use a proxy BUT: use 128.200.5.34 as a wais proxy, port 80 (but with patience there are some bugs in the proxy code that I'm also trying to work out - sometimes it works fine, other times it times out or fails completely, due to the default behavior of re-proxying thru Switzerland - due to change as soon as I can figure it out. Dedicated wais clients such as waissearch, swais, WAIStation, Xwais, MacWAIS, WAIS for Mac, WinWAIS, etc, available from ftp://ftp.wais.com/pub/freeware (I have also built some Linux clients with the freewais dist). Gopher - Some gophers also recognize WAIS src files as such and will respond appropriately when pointed at them. Cost is free in return for bug reports and comments.... Cheers harry -- Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 --- knowledge is fractal --- http://hornet.mmg.uci.edu/~hjm/hjm.html Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!usc!nic-nac.CSU.net!csulb.edu!paris.ics.uci.edu!news.service.uci.edu!buggus.mmg.uci.edu!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: RNA folding programs Date: Fri, 03 Mar 1995 09:19:40 -0800 Organization: Microbiology and Molecular Genetics, UC Irvine Lines: 28 Message-ID: References: <3j24f4$h3g@netnews.upenn.edu> NNTP-Posting-Host: buggus.mmg.uci.edu In article <3j24f4$h3g@netnews.upenn.edu>, lynnanne@blue.seas.upenn.edu (Lynn Anne Sanguedolce) wrote: > Bio-software users: > > I am interested in finding out what programs for MAC are available to predict > RNA and/or single strand DNA folding. Does anyone know of particular > programs and where to find them? > > Thank you, > Lynn Anne Sanguedolce > > Department of Chemical Engineering > University of Pennsylvania > lynnanne@eniac.seas.upenn.edu Check out: http://hornet.mmg.uci.edu/~hjm/projects/biocomp/rna.folding.html You're welcome. hjm -- Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 --- knowledge is fractal --- http://hornet.mmg.uci.edu/~hjm/hjm.html Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: Graph maker for Mac Date: 3 Mar 1995 16:58:36 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 14 Message-ID: <3j7hrs$1b7l@sat.ipp-garching.mpg.de> References: NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] Takuya Maemoto (T.Maemoto@ed.ac.uk) wrote: > Could anybody recommend any graph package with curve fit function for Mac? Maybe Kaleidagraph might work for you. BTW, what do you mean with "detail of fitting"? Cricket Graph reports about the obtained parameters with errors. --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "Science is the game you play with God to find out what His rules are." */ From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!ns1.faseb.org!darwin.sura.net!udel!gatech!howland.reston.ans.net!news.sprintlink.net!uunet!sunic!news.uni-c.dk!news.daimi.aau.dk!biobase!wind From: wind@biobase.dk (Troels Wind) Newsgroups: bionet.software Subject: WANTED: htlm filter for Word6.0 Date: 3 Mar 1995 10:42:49 GMT Organization: The Danish BioBase Lines: 16 Message-ID: <3j6rr9$4im@biovax.biobase.dk> NNTP-Posting-Host: biobase.dk X-Newsreader: TIN [version 1.2 PL2] Hi netters, I know it's a bit misplaced to post this in bionet, but it's the computer- related newsgroup I subscribe to, so here it comes... In near future I have to present a page on WWW, so I need a filter for translating RTF to HTLM. I already have one (RTFTOHTLM), but I'm looking for one that will fonktion as a 'plug-in' in Word6.0 for the Macintosh. I KNOW it's outthere somewhere, could anybody please give me the adress, ftp-site ore whatever?? Thanks! Troels Wind From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!udel!helios!landel From: landel@helios (Carlisle Landel) Newsgroups: bionet.general,bionet.molbio.methds-reagnts,bionet.software Subject: Re: Univ. charging $100/mo./person for mainframe access Date: 3 Mar 1995 16:05:12 GMT Organization: Alfred I. DuPont Institute, Wilmington DE USA Lines: 37 Message-ID: <3j7eno$ovi@louie.udel.edu> References: <3ilglt$c96@cronkite.ocis.temple.edu> <3j0qqc$8rc@news.doit.wisc.edu> <3j56g3$oc6@gap.cco.caltech.edu> NNTP-Posting-Host: helios.medsci.udel.edu Xref: biosci bionet.general:13941 bionet.molbio.methds-reagnts:25380 bionet.software:11330 In article <3j56g3$oc6@gap.cco.caltech.edu>, wrote: >In article <3j0qqc$8rc@news.doit.wisc.edu>, Michael Kloth writes: >>gold@astro.ocis.temple.edu (Bert Gold) wrote: >>> >>> One of the universities where I work has decided to charge $ 100 per >>> person per month for mainframe access. As everyone in these newsgroups >>> knows, this kind of access is an absolute requirement for doing >>> molecular biology in 1995! >> >>The University of Wisconsin in Madison not only does not charge > >This is very misleading. They may not bill for direct usage, but they most >definitely are charging someone, somewhere, for this facility. Most likely >it is supported by a combination of University overhead charges against >research grants and charges against students' tuition. They might also have >a direct grant to run it, but that seems kind of unlikely for a central >computing facility. > [a list of what your computer facility does for you followed] Look, somebody has to pay for the facility. And they offer a bunch of services. But you do have *other* options. If you feel that all you need is a connection to the internet, then go out and buy yourself one! I understand you can get them for $20-$40 a month--all you need is a modem and a phone line. Yeah, I know, it's still a precious $20- $40 a month out of your hard-earned grant dollars, but it's better than $100/month. Everything you need to do is most likely accomplished on a mac or pc on your desk, so you don't need the central facility, anyway. But if you do need them, then you should be willing to pay\ for it. (Now, if the institution is already billing the feds overhead for computer services, that's another story.) Carlisle Landel --who, on re-reading what he has written, is horrified to discover that he sounds like some kind of wild-eyed free marketeer--yikes! ;) From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!Germany.EU.net!news.dfn.de!zeus.rbi.informatik.uni-frankfurt.de!terra.wiwi.uni-frankfurt.de!news.th-darmstadt.de!hrz-ws11.hrz.uni-kassel.de!hrz-ws28.hrz.uni-kassel.de!bartke From: bartke@hrz-ws28.hrz.uni-kassel.de (C. R. Bartke) Newsgroups: bionet.software Subject: Re: RNADRAW: Help. Date: 3 Mar 1995 11:32:33 GMT Organization: Kassel University, Germany Lines: 17 Distribution: world Message-ID: <3j6uoh$hu5@hrz-ws11.hrz.uni-kassel.de> References: <1995Feb24.143509.1@samba.cnb.uam.es> Reply-To: bartke@hrz.uni-kassel.de NNTP-Posting-Host: hrz-ws28.hrz.uni-kassel.de In article <1995Feb24.143509.1@samba.cnb.uam.es>, pgomez@samba.cnb.uam.es (PAULINO GOMEZ PUERTAS. CISA-INIA. VALDEOLMOS. 28130, MADRID.) writes: |> Could anybody help me? There is another program that generates the |> "rnafold output files"? Try 'experimenting' with the RIGHT mouse button and click on the RNA- sequence windows. Hope this helps ... ___________________________________________________________________ Cornelius R. Bartke Student der Biologie im FB 19 Hauffstrasse 16 Gesamthochschule Universit„aet Kassel 34246 Vellmar Kassel - Germany Fon&Fax: ++49/561/823330 e-mail: bartke@hrz.uni-kassel.de From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!Norway.EU.net!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!reuter.cse.ogi.edu!netnews.nwnet.net!ns1.nodak.edu!beangenes.cws.ndsu.nodak.edu!mcclean From: mcclean@PROBLEM_WITH_INEWS_DOMAIN_FILE (Phil McClean) Subject: Linux version of Mapmaker Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Fri, 3 Mar 1995 22:26:24 GMT Nntp-Posting-Host: beangenes.cws.ndsu.nodak.edu Organization: I need to put my ORGANIZATION here. X-Newsreader: TIN [version 1.2 PL2] Lines: 14 [ Article crossposted from bionet.molbio.rapd ] [ Author was Phil McClean ] [ Posted on Fri, 3 Mar 1995 15:20:24 GMT ] Does anyone know if a version of Mapmaker compiled for Linux exists anywhere? If so, please let me know, I would like to get a copy of it. Phil McClean Dept. of Plant Sciences North Dakota State University Fargo, ND 58105 mcclean@beangenes.cws.ndsu.nodak.edu From owner-software@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!rutgers!uwm.edu!post.its.mcw.edu!not-for-mail From: ckrepel@post.its.mcw.edu (Candace Krepel) Newsgroups: bionet.general,bionet.molbio.methds-reagnts,bionet.software Subject: Re: Univ. charging $100/mo./person for mainframe access Followup-To: bionet.general,bionet.molbio.methds-reagnts,bionet.software Date: 3 Mar 1995 10:37:25 -0600 Organization: Medical College of Wisconsin; Milwaukee Wisconsin Lines: 14 Distribution: world Message-ID: <3j7gk5$bof@post.its.mcw.edu> References: <3ilglt$c96@cronkite.ocis.temple.edu> NNTP-Posting-Host: post.its.mcw.edu X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.general:13942 bionet.molbio.methds-reagnts:25390 bionet.software:11331 Bert Gold (gold@astro.ocis.temple.edu) wrote: : One of the universities where I work has decided to charge $ 100 per : person per month for mainframe access. As everyone in these newsgroups : knows, this kind of access is an absolute requirement for doing : molecular biology in 1995! I suspect that the maintenance charges, costs for purchase, upgrade, etc. of hard- and software are already being passed on to the various departments as part of the infamous *university overhead*. If the school is going to separate out mainframe costs and bill separately, I doubt that the overhead costs will go down accordingly. Candy Krepel ckrepel@post.its.mcw.edu From owner-software@net.bio.net Fri Mar 03 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!uunet!psinntp!rebecca!tethys.ph.albany.edu!TIVOL From: tivol@tethys.ph.albany.edu Newsgroups: bionet.general,bionet.molbio.methds-reagnts,bionet.software Subject: Re: Univ. charging $100/mo./person for mainframe access Date: 3 Mar 1995 19:36:20 GMT Organization: SUNYA School of Public Health, Albany, NY Lines: 60 Message-ID: <3j7r3k$dpv@rebecca.albany.edu> References: <3ilglt$c96@cronkite.ocis.temple.edu>,<3j0qqc$8rc@news.doit.wisc.edu>,<3j56g3$oc6@gap.cco.caltech.edu> Reply-To: tivol@tethys.ph.albany.edu NNTP-Posting-Host: tethys.ph.albany.edu Xref: biosci bionet.general:13970 bionet.molbio.methds-reagnts:25448 bionet.software:11342 In article <3j56g3$oc6@gap.cco.caltech.edu>, mathog@seqaxp.bio.caltech.edu writes: >In article <3j0qqc$8rc@news.doit.wisc.edu>, >Michael Kloth writes: >>gold@astro.ocis.temple.edu (Bert Gold) wrote: >>> >>> One of the universities where I work has decided to charge $ 100 per >>> person per month for mainframe access. > >This is very misleading. They may not bill for direct usage, but they most >definitely are charging someone, somewhere, for this facility. Most likely >it is supported by a combination of University overhead charges against >research grants and charges against students' tuition. Since this is probably true at all sites, it seems very restrictive to charge the user $100/person/month in addition for access to a necessary resource. > >Academic computer facility users have an annoying habit of assuming that >[snip] there are no significant costs involved in providing these services. Not those of us who use our internal computer facilities as well as those silicon things. > >So, here is a short list of what your local computer support people do for >you: That's why we pay them the big money. > >1. Purchase, install and maintain the hardware that makes up your > local networks. With our grant money, in many cases. >7. (some sites) Computer hardware/software sales and support at prices > lower than general market rates. Well, they *did* turn me on to "Computer Shopper" > >8. Purchase, install, and maintain shared hardware. (Generally > Unix or VMS machines, but also sometimes PCs and Macs.) Again, with our grant money. >I've left a bunch of stuff off and been overly general in others. Note >also that a lot of the PC/Mac freeware/shareware was developed by the >people who run these sorts of facilities! Yes, and I, for one am grateful. > >The bottom line: equipment and services cost real money. > True, but is that any reason for anyone to be greedy? A previous post suggest- ed that internet access was available from commercial companies for less, and these companies do not get indirect costs from our grants. You have a real point that the benefits some of us get may not be fully appreciated, but there is no reason (except that universities everywhere are in desperate need of $) to try to gouge internet users. Yours, Bill Tivol From owner-software@net.bio.net Fri Mar 03 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!holzwarth3.life.uiuc.edu!user From: jbuberel@uiuc.edu (Jason L. Buberel) Newsgroups: bionet.software Subject: Re: NIH Image Date: Sat, 04 Mar 1995 09:36:20 -0600 Organization: Universtiy of Illinois Lines: 28 Distribution: world Message-ID: References: NNTP-Posting-Host: holzwarth3.life.uiuc.edu In article , Paul-pottorff@uiowa.edu (Paul Pottorff) wrote: > Hey Guys > > Does anyone know where I can find detailed help documents on NIH Image. I > retreived the program from Zippy... but I could not find any detailed help > files there. > > thanks > Paul paul, on zippy.nih.gov, there is a docuemtation file, ftp://zippy.nih.gov/pub/image/nih-image156_docs.hqx for you to download. -jason ================ Jason L. Buberel Graduate Student Nueroscience Pgm U of Illinois-UC ================ From owner-software@net.bio.net Fri Mar 03 22:00:00 1995 Path: biosci!rutgers!gatech!swrinde!cs.utexas.edu!news.sprintlink.net!uunet!cis.ohio-state.edu!magnus.acs.ohio-state.edu!mail-news-gateway From: zollmann.1@osu.edu (Frank S. Zollmann) Newsgroups: bionet.software,bionet.cellbiol Subject: HUM-MOLGEN: COMPUTERS 9/95 Date: 3 Mar 1995 22:30:09 -0500 Organization: The Ohio State University Lines: 258 Sender: root@magnus.acs.ohio-state.edu Message-ID: <199503040328.WAA25858@postbox.acs.ohio-state.edu> NNTP-Posting-Host: charm.magnus.acs.ohio-state.edu Xref: biosci bionet.software:11338 bionet.cellbiol:1741 HUM-MOLGEN COMPUTERS TOPIC introduce interesting Internet resources (see example) and is open for discussions in the field of Computational Genetics. Please mail your suggestions for Internet-Highlights to HUM-MOLGEN@nic.surfnet.nl (Subject: COMP: ...). To subscribe this free service, send message subscribe HUM-MOLGEN first_name last_name to listserv@nic.surfnet.nl. Frank S. Zollmann (Editor HUM-MOLGEN) ****HUM-MOLGEN IS......... HUM-MOLGEN is a general interest communication-list in Human (Molecular) Genetics. The purpose of the list is to create a world-wide communication-forum in Genetics. ****SUBSCRIBERS ARE....... Subscribers to the list are molecular biologists, geneticists, clinicians, biology and medical students and other individuals interested in the field of Human Genetics. ************************************************************************ HUM-MOLGEN: COMPUTERS 9/95 ************************************************************************ This COMPUTERS message introduces 3 interesting Internet resources 1) The DICTIONARY of CELL BIOLOGY, published by Academic Press, is available free for searching on the WWW. 2) A March 1, 1995 update of The Medical List is now available from the Univ. of Michigan Clearinghouse 3) CancerNet last revised: March 1, 1995. CancerNet is a quick and easy way to obtain, through electronic mail, cancer information from the National Cancer Institute (NCI) ************************************************************************ 1) The second edition of The DICTIONARY of CELL BIOLOGY, published by Academic Press, is available free at http://130.209.9.190/. The server contains 5450 entries and 5772 cross-references. ************************************************************************ 2) A March 1, 1995 update of The Medical List is now available from the Univ. of Michigan Clearinghouse for Subject Oriented Guides URL:gopher://una.hh.lib.umich.edu:70/00/inetdirsstacks/medclin:malet The Medical List is a database of clinical medicine Internet resources. This new and improved version categorizes resources by disease and specialty. It subcategorizes the resources as web or interactive resources. This new version lists more than 60 new entries. The Medical List gives text descriptions of resources, spotlights the more developed programs, and gives news and backround on Internet medical resource development. The Medical List is made available in a Mosaic, hypertext, Internet-linked format as "Medical Matrix". Medical Matrix is available at the URL: http://kuhttp.cc.ukans.edu/cwis/units/medcntr/Lee/HOMEPAGE.HTML ************************************************************************ 3) To receive the whole document please send message help to: cancernet@icicb.nci.nih.gov // ... // = cut of parts of the message +----------------------------------------------+ | NATIONAL INSTITUTE | | C A N C E R | | INTERNATIONAL INFORMATION | | C E N T E R | +----------------------------------------------+ | cancernet@icicb.nci.nih.gov | +-------------------------------+ CancerNet last revised: March 1, 1995 CancerNet is a quick and easy way to obtain, through electronic mail, cancer information from the National Cancer Institute (NCI). CancerNet lets you request information statements from the NCI's Physician Data Query (PDQ) database, fact sheets on various cancer topics from the NCI's Office of Cancer Communications, and citations and abstracts on selected topics from the CANCERLIT database. Selected information is also available in Spanish. You can access CancerNet through a number of different networks including BITNET and Internet. There is no charge for the service unless your local computer center charges for use of e-mail. The CancerNet Contents List (included here) changes at the beginning of each month as new information is included. CancerNet is an automated system that reads standardized requests and then returns the requested information via electronic mail. CancerNet cannot respond to requests for information that is not found in the system, such as lists of clinical trials. If you have trouble using CancerNet, you may call 1-800-624-7890 (within the U.S.) or (301) 496-7600 (if outside the U.S.) or send a message to cheryl@icicb.nci.nih.gov on the Internet. Instructions 1. Address your mail message to: cancernet@icicb.nci.nih.gov [If you are not on Internet, you may have to change the format of the address. Consult with your systems manager for the correct address format.] 2. In the body of the message: Enter the CancerNet ID from the Contents List for the desired information. If you need the updated contents list, enter the word "help" in the body of the message ("spanish" if you want the Spanish contents list). If you want more than one piece of information, enter the code for each piece of information on a separate line within the message. Your request must be in the BODY of the message, not the subject line. You can type a subject for your message if you wish, but CancerNet will not read it. Examples: To receive the PDQ breast cancer statement for health professionals: To: cancernet@icicb.nci.nih.gov Subject: cn-100013 // ... // 3. End your message. If you requested multiple items within a single request, each item will be returned to you in a separate message. It usually takes about 10 minutes for you to receive your information, although delays in connections across the Internet may cause you to receive your request later. WARNING: Individual statements may exceed 100K and some mail systems are limited in the size of the mail messages a user can receive. Please check your mail and storage capacity prior to submitting requests. The information in CancerNet is updated monthly, and many items change from one month to the next. // ... // IF YOU ARE INTERESTED IN REGULARLY TRANSFERRING AND MAKING INFORMATION FROM CANCERNET AVAILABLE LOCALLY, PLEASE REQUEST STATEMENT CN-400030. THE NCI WILL FACILITATE SUCH ENDEAVORS, BUT CERTAIN CONDITIONS APPLY TO SUCH REDISTRIBUTION. ++++++++++++++++++++++++++++++ ++ CancerNet Contents List ++ ++++++++++++++++++++++++++++++ PDQ Statement List, which includes: PDQ Treatment Summaries for Health Professionals PDQ Treatment Summaries for Patients PDQ Supportive Care Summaries PDQ Cancer Screening/Prevention Summaries PDQ Drug Information Summaries CancerNet News and NCI Publication Information Fact Sheets from the NCI CANCERLIT Citations and Abstracts ************************ PDQ Statement List ************************ The following list gives all the PDQ statements available on CancerNet: treatment for health professionals and patients, supportive care, screening/prevention, and drugs. // ... // PDQ TREATMENT STATEMENTS DIAGNOSIS. . . . . . . . . . . . . . . . . .HEALTH PROF . . PATIENTS Adrenocortical Carcinoma . . . . . . . . . . .cn-101198 . . cn-201198 AIDS-Related Lymphoma. . . . . . . . . . . . .cn-103779 . . cn-203779 // ... // Vulvar Cancer. . . . . . . . . . . . . . . . .cn-101038 . . cn-201038 Wilms' Tumor . . . . . . . . . . . . . . . . .cn-100719 . . cn-200719 SUPPORTIVE CARE Constipation, Impaction, and Bowel Obstruction .cn-303510 Fatigue. . . . . . . . . . . . . . . . . . . . .cn-304461 // ... // Sleep Disorders. . . . . . . . . . . . . . . . .cn-304282 Superior Vena Cava Syndrome. . . . . . . . . . .cn-304708 CANCER SCREENING AND PREVENTION Overview Cancer Prevention. . . . . . . . . . . . . cn-304750 Cancer Screening . . . . . . . . . . . . . cn-303092 Aerodigestive Tract Cancer (head & neck, esophagus, lung) Prevention. . . . . . . . . . . . . . . . .cn-305233 // ... // Testicular Cancer Screening . . . . . . . . . . . . . . . . .cn-304729 INVESTIGATIONAL DRUGS Aminocamptothecin (9-AC) . . . . . . . . . . . .cn-804975 Buthionine sulfoximine . . . . . . . . . . . . .cn-801713 // ... // Topotecan. . . . . . . . . . . . . . . . . . . .cn-804259 Tretinoin (TRA). . . . . . . . . . . . . . . . .cn-804331 OTHER PDQ INFORMATION Design of Clinical Trials. . . . . . . . . . . .cn-303901 . . . .cn-203900 // ... // CancerNet News: Information About CancerNet, PDQ, and Related Services ----------------------------------------------------------------------- Information About PDQ# . . . . . . . . . . . . . . . . . . .cn-400001 Redistribution of CancerNet and CancerNet Availability . . .cn-400030 // ... // *NOTE: Files that are marked with an ASTERISK (*) can only be obtained through CancerFax. Use the following instructions to access CancerFax. +-----------------------------------------------------------------------+ | How do I use CancerFax? | | | | 1. Use only the 6 digits from the CancerNet code in the Contents | | List (drop the "cn-" in front of the code). | // ... // ******************* end of message ************************************* From owner-software@net.bio.net Fri Mar 03 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!scripps.edu!NewsWatcher!user From: Bibbs@scripps.edu (Lisa) Newsgroups: bionet.general,bionet.molbio.methds-reagnts,bionet.software Subject: Re: Univ. charging $100/mo./person for mainframe access Date: 4 Mar 1995 00:38:28 GMT Organization: The Scripps Research Institute, La Jolla, CA Lines: 6 Message-ID: References: <3ilglt$c96@cronkite.ocis.temple.edu> <3j0qqc$8rc@news.doit.wisc.edu> <3j2o89$anb@news.doit.wisc.edu> NNTP-Posting-Host: bertha.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Xref: biosci bionet.general:13953 bionet.molbio.methds-reagnts:25427 bionet.software:11337 While I think $100/mo/person is excessive, I understand that to keep up with the hardware and software changes on the computer industry some fees are necessary. I don't think a computer department's slice of NIH overhead charges could cover some of the equipment purchases that are necessary to keep us all up to date. Lisa From owner-software@net.bio.net Fri Mar 03 22:00:00 1995 Newsgroups: bionet.software Path: biosci!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: More WWW sites (Re: cool and funky WWW site) Message-ID: <1995Mar4.165236.14284@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: Date: Sat, 4 Mar 1995 16:52:36 GMT Lines: 31 ewan birney (birney@molbiol.ox.ac.uk) wrote: : Excuse the gratuitous subject! done :-) : I'm trying to write (in spare moments) a CUSI version for : biological databases over the web. (?? call it a bioCUSI?) There is already a really comprehensive collection of sites - all in all, 69 databanks at 11 servers. Look at http://www.embl-heidelberg.de/srs/srsc (this is Thure Etzold's SRS server system). The big pain of the biological database arena is that there are so many similar and interlinked databases that an individual retrieval is no longer the most desirable thing to do. Rather, the INTERLINKING of these data is the main issue. Alternatively, COMBINING queries is required - e.g., do two searches and get only those which show up as results in both. The URL mentioned above (http://www.embl-heidelberg.de/srs/srsc) gets you into a database web system which does precisely that. The queries written by Ewan have not even half of that functionality - and surely much less databases. Regards Reinhard Doelz -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-software@net.bio.net Fri Mar 03 22:00:00 1995 Newsgroups: bionet.software Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!news From: ewan birney Subject: cool and funky WWW site Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Fri, 3 Mar 1995 17:06:19 GMT Organization: European Bioinformatics Institute Lines: 28 Excuse the gratuitous subject! I'm trying to write (in spare moments) a CUSI version for biological databases over the web. (?? call it a bioCUSI?) look at http://www.ocms.ox.ac.uk/~birney/cusi/cusi.html I've put in all the sites which I usually normally - however there are *many* more. If you want to let me know what database *you* would like to see then email me. In fact there is a comment form which sends email directly to me for the people too lazy even to pull down another window... gripes, complaints, comments etc welcome. (if anyone wants to set it up on their server it is very easy... - as long as you're running perl - email me or just pull down CUSI for www.nexor.co.uk) ewan birney birney@molbiol.ox.ac.uk http://www.ocms.ox.ac.uk/~birney/me.html From owner-software@net.bio.net Fri Mar 03 22:00:00 1995 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!lll-winken.llnl.gov!noc.near.net!plato.simons-rock.edu!preacher From: preacher@plato.simons-rock.edu (Care Michaud) Subject: L-SYSTEM, 3D FLOWERS X-Newsreader: TIN [version 1.2 PL2] Organization: Simon's Rock College Message-ID: Date: Sat, 4 Mar 1995 21:30:56 GMT Lines: 13 By following many peoples suggestions, I visited the University of Calgary's www site, and was dualy impressed. Now that I'm intrigued, I'm also frustrated. There seems to de a distinct lack of 3D L-System programs for the Mac. Am I mistaken, or is PFG the only program for the mac (its a 2D implimentation of L-System)? Where can I find other programs, or other sites that contain info on morphogenisis. Also does anyone know of an ftp site that contains 3D flower models? Thanks -Care Michaud From owner-software@net.bio.net Sat Mar 04 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: Linux version of Mapmaker Date: 5 Mar 1995 10:12:35 GMT Organization: University of Cambridge, England Lines: 25 Message-ID: <3jc2qj$2oi@lyra.csx.cam.ac.uk> References: NNTP-Posting-Host: mole.bio.cam.ac.uk mcclean@PROBLEM_WITH_INEWS_DOMAIN_FILE (Phil McClean) writes: >[ Article crossposted from bionet.molbio.rapd ] >[ Author was Phil McClean ] >[ Posted on Fri, 3 Mar 1995 15:20:24 GMT ] > Does anyone know if a version of Mapmaker compiled for Linux exists >anywhere? If so, please let me know, I would like to get a copy of >it. Is the source code freely available? If so, compiling it yourself shouldn't be too difficult. I have compiled large amounts of software for my Linux machine without too much difficulty. The problem is that if Mapmaker is a commercial product, you may find the company unwilling to port it (despite the fact that Linux almost certainly has far more users now than many of the commerical PC unices, such as SCO). However, all is not lost! If you can get hold of a SCO binary, you can try running it under the Linux iBCS kernel module. Many (but not all) SCO binaries will run under this, as long as they are statically linked (so you'd better have plenty of RAM). I have certainly run the SCO versions of WordPerfect and Xess3 on my Linux PC that way. Tim. From owner-software@net.bio.net Sat Mar 04 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software Subject: Re: Isoelectric points Date: 5 Mar 1995 00:31:41 -0000 Lines: 36 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3jb0pd$cd3@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk > >I'm looking for a utility, or code fragment, that estimates the isoelectric >points of proteins from IUPAC (single-character) amino acid sequences. > Hi, Here is a copy of an "old" posting. We fetched this program. Works just fine. Good luck, Jean-Loup --------------------------------------------------------------------- Jean-Loup Risler Tel: (33 1) 69 82 31 34 CNRS Fax: (33 1) 69 07 49 73 Centre de Genetique Moleculaire Email: risler@cgmvax.cgm.cnrs-gif.fr 91198 Gif sur Yvette Cedex France --------------------------------------------------------------------- ####################################################################### >Subject: pi program available > >A program for calculating the theoretical pI of a protein or >polypeptide has been written by Arthur David Olson of the >Laboratory of Experimental Carcinogenesis, NCI/NIH. It is available >by anonymous ftp to elsie.nci.nih.gov, as pub/pi.shar.gz. The program >is based on the paper by Sillero, A. and J. M. Ribeiro, "Isoelectric >points of proteins: theoretical determination,", Anal. Biochem., >vol. 179, no. 2, pp. 319-25, 1989. The manual and source are included. > From owner-software@net.bio.net Sat Mar 04 22:00:00 1995 Path: biosci!agate!library.ucla.edu!csulb.edu!nic-nac.CSU.net!charnel.ecst.csuchico.edu!waldorf.csc.calpoly.edu!decwrl!tribune.usask.ca!canopus.cc.umanitoba.ca!newsflash.concordia.ca!vega!l_zhang From: l_zhang@vega.concordia.ca (Lucie) Newsgroups: bionet.software Subject: Molecular biology software for Windows available Date: 5 Mar 1995 22:29:59 GMT Organization: Concordia University, Montreal, Canada Lines: 48 Message-ID: <3jde17$2ue@newsflash.concordia.ca> NNTP-Posting-Host: vega.concordia.ca NNTP-Posting-User: l_zhang X-Newsreader: TIN [version 1.2 PL2] A molecular biology software, DNAMAN version 2.2 for Windows is now available. DNAMAN is a multiple document application, which allows user to simultaneously work on different sequences and perform different analysis. Principal features of this package: 1) flexible sequence format: any sequence file using DOS text format (PC/Gene, DNASIS ...) direct access to GenBank file (introns may be automatically removed) 2) all necessary functions for DNA sequence manipulation 3) restriction analysis 4) drawing restriction map 5) restriction pattern prediction and DNA cloning 6) multiple alignment of DNA and/or protein sequences 7) dot-matrix comparison of DNA sequences 8) automatic assembly of DNA sequencing fragments 9) enhanced motif search in sequence and database 10) protein translation and codon usage analysis 11) protein hydrophobicity profile 12) PCR primer design and primer characterization Free demonstration version of DNAMAN is available upon requirement from: Lynnon BioSoft 88, rue Adam Vaudreuil-Dorion, Quebec Canada J7V 8P5 Fax: (514) 455-4269 From owner-software@net.bio.net Sat Mar 04 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: WPDB for MAC... Date: 5 Mar 1995 20:54:17 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 19 Distribution: world Message-ID: <3jd8dp$2f79@sat.ipp-garching.mpg.de> References: <9502281658.AA19173@helix.nih.gov> NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] Geetha Vasudevan (geetha@HELIX.NIH.GOV) wrote: > I would like to know if the PC based software WPDB is now > available for MAC. Thanks for any info. Not as far as I know. However, I do not see the advantage of WPDB to any PDB subset used together with a PDB viewer, such as Rasmol. Am I missing something here? (The problem seems to be that there is no easy way to download a sensible PDB subset ...) (BTW, WPDB is "The Protein Data Bank for Windows".) --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "Science is the game you play with God to find out what His rules are." */ From owner-software@net.bio.net Sat Mar 04 22:00:00 1995 Path: biosci!agate!newsxfer.itd.umich.edu!gatech!taco.cc.ncsu.edu!bgkerman From: bgkerman@eos.ncsu.edu (Bahram G Kermani) Newsgroups: bionet.software Subject: NEEDED: various software, hardware, videos, etc. for biosensor eng. Date: 5 Mar 1995 16:17:26 GMT Organization: North Carolina State University, Project Eos Lines: 53 Distribution: world Message-ID: <3jco6m$jla@taco.cc.ncsu.edu> Reply-To: bgkerman@eos.ncsu.edu (Bahram G Kermani) NNTP-Posting-Host: c11120-359dan.ece.ncsu.edu Keywords: software, biology, biosensory, senosry, hardware, lab, laboratory, experiment, Originator: bgkerman@c11120-359dan.ece.ncsu.edu optical, enzyme, biochemistry, biocompatibility, diagnosis, immunosensor, cytotoxicity Hi world, I am trying to gather up some experiments for a lab., and I would be very interested in getting/purchasing some relevant information (any media: Videos, slides, software, hardware), as teaching aids: I appreciate it very much, if you could give me your recommendations. Please answer by email (bahram@ncsu.edu) as I don't check this newsgroup very often. < Money is not a big issue! > Thanks, Bahram *********************************************************** The labs should fall into the following categories: 1. Enzymatic sensor machanisms 2. Optical biosensors 3. Protein sysnthesis nad genetic engineering 4. Fundamentals of cell biology 5. Biochemistry of membranes and receptors 6. Natural sensors and nervous receptors 7. Immunosensors 8. Microbial sensors 9. Living tissue and cells for signal acquisition 10. Biocompatibility 11. Pharmacological Modification of surfaces 12. Cytotoxicity and mutagenicity testing 13. Industrial biosensors 14. Pollution testing and control 15. Clinical diagnosis 16. Cardiovascular systems 17. Chemosensory systems From owner-software@net.bio.net Sat Mar 04 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!gatech!taco.cc.ncsu.edu!bgkerman From: bgkerman@eos.ncsu.edu (Bahram G Kermani) Newsgroups: bionet.software Subject: NEEDED: various software, hardware, videos, etc. for biosensor eng. Date: 5 Mar 1995 16:16:50 GMT Organization: North Carolina State University, Project Eos Lines: 53 Distribution: world Message-ID: <3jco5i$jl4@taco.cc.ncsu.edu> Reply-To: bgkerman@eos.ncsu.edu (Bahram G Kermani) NNTP-Posting-Host: c11120-359dan.ece.ncsu.edu Keywords: software, biology, biosensory, senosry, hardware, lab, laboratory, experiment, Originator: bgkerman@c11120-359dan.ece.ncsu.edu optical, enzyme, biochemistry, biocompatibility, diagnosis, immunosensor, cytotoxicity Hi world, I am trying to gather up some experiments for a lab., and I would be very interested in getting/purchasing some relevant information (any media: Videos, slides, software, hardware), as teaching aids: I appreciate it very much, if you could give me your recommendations. Please answer by email (bahram@ncsu.edu) as I don't check this newsgroup very often. < Money is not a big issue! > Thanks, Bahram *********************************************************** The labs should fall into the following categories: 1. Enzymatic sensor machanisms 2. Optical biosensors 3. Protein sysnthesis nad genetic engineering 4. Fundamentals of cell biology 5. Biochemistry of membranes and receptors 6. Natural sensors and nervous receptors 7. Immunosensors 8. Microbial sensors 9. Living tissue and cells for signal acquisition 10. Biocompatibility 11. Pharmacological Modification of surfaces 12. Cytotoxicity and mutagenicity testing 13. Industrial biosensors 14. Pollution testing and control 15. Clinical diagnosis 16. Cardiovascular systems 17. Chemosensory systems From owner-software@net.bio.net Sat Mar 04 22:00:00 1995 Newsgroups: bionet.software Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!news From: ewan birney Subject: Re: More WWW sites (Re: cool and funky WWW site) Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Sat, 4 Mar 1995 20:03:04 GMT References: <1995Mar4.165236.14284@comp.bioz.unibas.ch> Organization: European Bioinformatics Institute Lines: 59 doelz@comp.bioz.unibas.ch (Reinhard Doelz) wrote: > > ewan birney (birney@molbiol.ox.ac.uk) wrote: > > : Excuse the gratuitous subject! > > done :-) > > : I'm trying to write (in spare moments) a CUSI version for > : biological databases over the web. (?? call it a bioCUSI?) > > There is already a really comprehensive collection of sites - all in all, > 69 databanks at 11 servers. Look at http://www.embl-heidelberg.de/srs/srsc > (this is Thure Etzold's SRS server system). > > The big pain of the biological database arena is that there are so many > similar and interlinked databases that an individual retrieval is no longer > the most desirable thing to do. Rather, the INTERLINKING of these data > is the main issue. Alternatively, COMBINING queries is required - e.g., do > two searches and get only those which show up as results in both. The > URL mentioned above (http://www.embl-heidelberg.de/srs/srsc) gets you > into a database web system which does precisely that. The queries written > by Ewan have not even half of that functionality - and surely much less > databases. > > Regards > Reinhard Doelz > > -- > R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| > Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| > Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| > EMBnet Switzerland:info@ch.embnet.org you are right: SRS is a really neat system - interlinking is crucial - and SRS is the only system that deals with that... but... SRS doesn't have archie/CUI_WWW/ other ftp/web indexes (which I do use) This little creature can be set up on any site running an http server and perl: with no overheads. It takes minimal time to set up and maintain. this thing can be configured to add in more sites that you yourself use. I want to get a better "gateway" between the bioCUSI thing and SRS - but I'm not quite sure how to rig it SRS can get confusing. (to lesser mortals like me). CUSI is quite cute - no pancea I'd agree for biological databases but I think it has its own little contribution to give to the world. :) ewan From owner-software@net.bio.net Sat Mar 04 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!pc14.cip.bwl.uni-muenchen.de!rfink From: rfink@cip.bwl.uni-muenchen.de (Robert Finkeldey) Newsgroups: bionet.software Subject: Re: html software Date: Sun, 5 Mar 1995 16:01:55 Organization: Leibniz-Rechenzentrum, Muenchen (Germany) Lines: 9 Distribution: world Message-ID: NNTP-Posting-Host: pc14.cip.bwl.uni-muenchen.de X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Look for *html* with ARCHIE and you ´ll get an ftp-site near to you Robert Finkeldey rfink@cip.bwl.uni-muenchen.de Computer Science Lab Faculty of Business Administration University of Munich Ludwigstr.28 RG Germany From owner-software@net.bio.net Sat Mar 04 22:00:00 1995 Path: biosci!BIHO.TAEGU.AC.KR!shjang From: shjang@BIHO.TAEGU.AC.KR (Sei-Heon Jang) Newsgroups: bionet.software Subject: (none) Date: 5 Mar 1995 02:21:20 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <199503051020.TAA07122@biho.taegu.ac.kr> NNTP-Posting-Host: net.bio.net subscribe From owner-software@net.bio.net Sat Mar 04 22:00:00 1995 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!alfa02.medio.net!netnews.nwnet.net!ns1.nodak.edu!hugo From: e_hugo@dsu1.dsu.nodak.edu (Eric R. Hugo) Subject: Re: Graph maker for Mac Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: <3jb1n5$9po_001@chem.dsu.NoDak.edu> Date: Sun, 5 Mar 1995 00:47:33 GMT References: Nntp-Posting-Host: hugo.chem.dsu.nodak.edu Organization: Dickinson State University X-Newsreader: News Xpress Version 1.0 Beta #3 Lines: 19 I recommend Kaleidagraph, very functional and the Academic discount in the US is $60.00. I've used it for everything from Michaelis-Menten kinetics to equilibrium denaturation modeling. Very nice. It can be obtained from: Synergy Software 2457 Perkiomen Ave. Reading PA 19606-9976 USA The email address for a contact in the company is Steve Wilson consult@consult.synergy.com Disclaimer: I don't work for Synergy , I'm just a happy user of Kaleidagraph // \\ // \\ // \\ // \\ // \\ // \\ // \\ Eric Hugo, Ph.D.// |:,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ e_hugo@dsu1.dsu.nodak.edu\ | | \\ // | | // \\ | | \\ // | | // \\ | | Asst. Professor, Biology \\ | :,\\': | // \\ | :,\\': | // \\ | Dickinson State University \\ // \\ // \\ // \\ // \\ Dickinson, ND 58601 |PGP 2.6 Key available from most key servers From owner-software@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!news.service.uci.edu!buggus.mmg.uci.edu!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: MOLBIO SOFT. SITES /LINUX SW Date: Mon, 06 Mar 1995 09:19:08 -0800 Organization: Microbiology and Molecular Genetics, UC Irvine Lines: 59 Message-ID: References: <1995Feb28.100846.50436@ucl.ac.uk> <3j75cf$8mi@owl.und.ac.za> NNTP-Posting-Host: buggus.mmg.uci.edu In article <3j75cf$8mi@owl.und.ac.za>, dace@shrike.und.ac.za (Roy Dace) wrote: > Andrew Martin (martin@bsm.bioc.ucl.ac.uk) wrote: > : Run the free Linux Unix clone on your new PC and you'll have access to the > : whole world of free Unix software. Have a look at > : http://sunsite.unc.edu/mdw/linux.html for information on Linux. > > Hi, > > I'm also a Linux user but I'm wondering if you've seen any software of > specific interest to molecular biologists available for the OS. I'm > specifically looking for a program to help select PCR primers and (for > a different project) a port of one which can do cladistic anaylsis. > of PCR RAPD's. I've "ported" Ladeanna Hillier/Phil Green's Oligo Selection Program OSP (text and X windows version) to Linux (essentially a straight recompile, commenting out some Linux-confusing X11 code). Someone has ported the GDE package to Linux, altho it may be a rev out of date; I believe the ACEdb package runs fine on Linux, essentially anything that requires std libs and POSIX-like system calls should compile OK on LInux (Higgins' clustal v/w, Prestridge's signalscan, Gilbert's READSEQ and now Seqpup (I think..haven't tried it yet), etc. Specifically excluded are any programs that use special libs or expect special hardware configurations (notably SGI's GL libs, and graphics hardware, although this should change soon with the release of OpenGL (the 'Open' version of SGI's GL, which allows previously SGI-only software runnable on Suns, HPs, DEC Alphas, etc) and PC implementations of 3D video hardware using the GLint chips and others. I would imagine that Joe Felsenstein's Phylip pkg ports over pretty easily as well, if he hasn't done it already ....ahhhh, it has been - it was at least partly written on it: from Joe hisself: Fourie Joubert asked if any molecular biology applications have been ported to Linux. I suspect nearly everything that is distributed as Unix C source will work fine. I use Linux on my laptop as one of the systems I develop my phylogeny package PHYLIP on, and the 3.5c version which is in C source code compiles and works with no problems. ----- Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195 Internet: joe@genetics.washington.edu (IP No. 128.95.12.41) Bitnet/EARN: felsenst@uwavm Mail me for more info... Cheers harry -- Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 --- knowledge is fractal --- http://hornet.mmg.uci.edu/~hjm/hjm.html Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW From owner-software@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.sprintlink.net!uunet!server.iadfw.net!usenet From: paytonp@iadfw.net Newsgroups: bionet.software Subject: horse racing Date: 6 Mar 1995 03:21:39 GMT Organization: Internet America, Dallas Texas Lines: 12 Message-ID: <3jdv43$cd3@server.iadfw.net> NNTP-Posting-Host: ppp141.iadfw.net X-Newsreader: AIR News 3.X (SPRY, Inc.) Attention all horse racing fans!!! We have the ultimate software for you!!!! Allows you to place bets, view stats, view race. Place up to 6 bets at a time - no bookie needed! Only $5 Please email: paytonp@iadfw.net See you at the races! From owner-software@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.sprintlink.net!uunet!server.iadfw.net!usenet From: paytonp@iadfw.net Newsgroups: bionet.software Subject: horse racing Date: 6 Mar 1995 03:20:57 GMT Organization: Internet America, Dallas Texas Lines: 12 Message-ID: <3jdv2q$cd3@server.iadfw.net> NNTP-Posting-Host: ppp141.iadfw.net X-Newsreader: AIR News 3.X (SPRY, Inc.) Attention all horse racing fans!!! We have the ultimate software for you!!!! Allows you to place bets, view stats, view race. Place up to 6 bets at a time - no bookie needed! Only $5 Please email: paytonp@iadfw.net See you at the races! From owner-software@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.cac.psu.edu!psuvm!kvi1 Organization: Penn State University Date: Sun, 5 Mar 1995 12:51:38 EST From: Kirk Iversen Message-ID: <95064.125138KVI1@psuvm.psu.edu> Newsgroups: bionet.software Subject: Re: Graph maker for Mac References: <3j7hrs$1b7l@sat.ipp-garching.mpg.de> Lines: 10 I don't know much about Kaleidagraph, but a friend of mine likes an older version of it compared to DeltaGraph. I understand that a demo disk is available from Synergy Software. E-mail address: hnath@info.synergy.com. Kirk V. Iversen Agronomy Department E-mail: kvi1@psuvm.psu.edu Penn State University Phone: 814/865-2119 University Park, PA 16802 From owner-software@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!nickel.ucs.indiana.edu!jlblue From: jlblue@nickel.ucs.indiana.edu (john blue) Newsgroups: bionet.drosophila,bionet.general,bionet.molbio.bio-matrix,bionet.molbio.gene-linkage,bionet.software,bionet.software.pc,sci.bio,sci.bio.technology Subject: Colony management software? Date: 6 Mar 1995 22:22:29 GMT Organization: Indiana University, Bloomington Lines: 20 Distribution: inet Message-ID: <3jg1v5$l03@usenet.ucs.indiana.edu> NNTP-Posting-Host: nickel.ucs.indiana.edu Xref: biosci bionet.drosophila:917 bionet.general:14012 bionet.molbio.bio-matrix:568 bionet.molbio.gene-linkage:596 bionet.software:11364 sci.bio:14733 sci.bio.technology:2412 Hi, I am trying to find software that will assist in the management of mice colonies. The software package or packages needs to be able to handle logistical information on groups of mice, breeding, genetic linkage, daily activities, etc. It would be nice if this software could be configured to run on portable machines so data collection would be less paper oriented. Also, the incorporation of bar-codes for data entry would be nice. Any leads would be appreciated, John Blue -- ------------------------------------------------------------------------------ John Blue, jlblue@indiana.edu Poplars Room 730 Computing Technology Assistance Center 400 East 7th Street 812-855-7530 Bloomington, Indiana 47405 From owner-software@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!sun1!tbr1105 From: tbr1105@sun1.lrz-muenchen.de (Hans-Georg Klieber) Newsgroups: bionet.software Subject: wanted: software to draw chemical structures Date: 6 Mar 1995 22:11:05 GMT Organization: Leibniz-Rechenzentrum, Muenchen (Germany) Lines: 8 Distribution: world Message-ID: <3jg19p$kkr@sunserver.lrz-muenchen.de> NNTP-Posting-Host: sun1.lrz-muenchen.de I need a windows program to draw chemical graphs and structures. Thanks a lot for any hints and pointers. Hans-Georg Klieber Physiology Department University of Marburg, Germany From owner-software@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!udel!news.sprintlink.net!uunet!server.iadfw.net!usenet From: paytonp@iadfw.net Newsgroups: bionet.software Subject: apology to all Date: 6 Mar 1995 20:19:37 GMT Organization: Internet America, Dallas Texas Lines: 6 Message-ID: <3jfqop$8eu@server.iadfw.net> NNTP-Posting-Host: ppp143.iadfw.net X-Newsreader: AIR News 3.X (SPRY, Inc.) Very sorry to have offended so many people with my ad for the horse racing software. I didn't realize my first week on internet I would make so many enemies--regretfully sorry. I would love to remove my offending ad- but am having trouble doing so. If someone would be so kind as to share with me instructions for deleting it I will be glad to get rid of it. Once again, i didn't mean to offend. Thanks. From owner-software@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!zeus.rbi.informatik.uni-frankfurt.de!terra.wiwi.uni-frankfurt.de!news.th-darmstadt.de!News.Uni-Marburg.DE!usenet From: becker@ps1515.chemie.uni-marburg.de (Anderas Becker) Newsgroups: bionet.software Subject: Re: NIH Image for Windows Date: 6 Mar 1995 00:52:06 GMT Organization: FB Chemie/Biochemie Lines: 20 Message-ID: <3jdmbn$473@surz03.HRZ.Uni-Marburg.DE> References: <1995Feb20.165923.730@titan.sfasu.edu> <3j42ut$5kb@sunserver.lrz-muenchen.de> NNTP-Posting-Host: nnex01.ppp.uni-marburg.de X-Newsreader: WinVN 0.92.6+ In article <3j42ut$5kb@sunserver.lrz-muenchen.de>, u735101@sun1.lrz-muenchen.de () says: > >>If it exists, does anyone know how and/or where I can get a copy of NIH Image for Windows? Email or >>direct post will be much appreciated. > >Does not exist! It is only available for (Power)Macs. > >--Harald Felgner > But you can run NIH-Image V1.55 with executor unter DOS. It is a shareware emulation for a mac. Find version 199k (or may be 1.2) of executor and install version 1.55 of NIH-Image. You find that "old" version of NIH-Image in the spin_offs directory of the zippy server. If you have more questions do not bother to ask me. I had had to solve the same problem. ---------------------------------------------------------------------- Andreas Becker Arbeitskreis Prof. Kadenbach, FB Chemie/Biochemie, Hans- Meerwein-Strasse, Philipps-Universitaet, 35043 Marburg, Germany Phone: privat +49 6421 47304 Labor +49 6421 28 -5721 Fax -2191 eMail: BECKER@ps1515.Chemie.Uni-Marburg.De From owner-software@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!pipex!penny.ibmpcug.co.uk!kate.ibmpcug.co.uk!tschues!luke Newsgroups: bionet.software Message-ID: <37@tschues.win-uk.net> Reply-To: luke@tschues.win-uk.net (Lukas Heukamp) From: luke@tschues.win-uk.net (Lukas Heukamp) Date: Mon, 06 Mar 1995 17:37:18 GMT Subject: how to draw plasmids Lines: 8 Whenever I am writing-up experiments in Molecular-Biology I have trouble drawing circular plasmid represenations as this is very difficult to do on ordinary graphics programms for PCs. I am looking for some more useful programms to do the job.. and would welcome any suggestions on which ones to use and where to get them. Thank you for your help Lukas Heukamp From owner-software@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!newsxfer.itd.umich.edu!zip.eecs.umich.edu!panix!news.columbia.edu!sawasdee.cc.columbia.edu!ps44 From: Pavel Sova Newsgroups: bionet.software Subject: What hardware for image processing? Date: Mon, 6 Mar 1995 10:57:14 -0500 Organization: Columbia University Lines: 42 Message-ID: NNTP-Posting-Host: sawasdee.cc.columbia.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: ps44@sawasdee.cc.columbia.edu Hi, Sorry for this newbie question, but here it comes: Our boss is willing to buy a Power Mac system, among other purposes for image processing. I would like to know your suggestions about hardware needed; resp. what image board (frame graber) is recommended for capturing still images of gels and autoradiography films (and then analyzing them by NIH Image program and assembling into publication - grade pictures in some other aplication [something like Paintshop Pro, perhaps?]). I am new into this area (as well as I've never used Mac) - your recommendation (brands and prices) will be very wellcome. In ftp site for NIH-Image I found relevant part of faq: > 6. We may have a chance to purchase a computer to run NIH Image. What > would be the best board to have for digitizing images [we find > QuickCapture slow and inflexible due to no gain control]? > The Scion LG-3 has software gain and offset control but is not any > faster the QuickCapture card. Both the LG-3 and QuickCapture are > noticabley faster on Macs using built-in video because of the faster > data path to video RAM. Are these image boards (frame grabers)? And how much do they cost? Also, is IBM-compatible system setup better for this? We have an older camera Microcomp (Southern Micro Instruments), supposedly of a good quality, with good Sony video monitor. Thank you in advance, Pavel ----------------------------------------------------- Pavel Sova e-mail: Molecular Virology Laboratory ps44@columbia.edu Columbia University New York ----------------------------------------------------- From owner-software@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!news.cs.umb.edu!hsdndev!purdue!haven.umd.edu!hecate.umd.edu!usenet From: bwilliam@oyster.smcm.edu (Bill Williams) Newsgroups: bionet.software Subject: Re: Anybody using Labview?(data aquisition/control) Date: 6 Mar 1995 19:30:09 GMT Organization: St. Mary's College of Maryland Lines: 9 Message-ID: <3jfns2$47g@umd5.umd.edu> References: <3j494m$8af@news.asu.edu> NNTP-Posting-Host: williams.smcm.edu X-Posted-From: InterNews 1.0.6@williams.smcm.edu X-Authenticated: bwilliam on POP host oyster.smcm.edu There is a discussion list for Labview. Contact Tom Coradeshi, TCORA@pica.army.mil for more information. _______________________________ Bill Williams bwilliam@oyster.smcm.edu Dept. of Biology St. Mary's College of Maryland St. Mary's City, MD 20686 USA From owner-software@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!agate!newsxfer.itd.umich.edu!gatech!swrinde!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-konstanz.de!chclu.chemie.uni-konstanz.de!AW1 From: aw1@chclu.chemie.uni-konstanz.de Newsgroups: bionet.software Subject: surface-maths Date: 6 Mar 1995 09:09:04 GMT Organization: Univ.Konstanz,Germany Lines: 8 Distribution: world Message-ID: <3jejfg$6av@eurybia.rz.uni-konstanz.de> Reply-To: aw1@chclu.chemie.uni-konstanz.de NNTP-Posting-Host: dg3.chemie.uni-konstanz.de I am looking for a program that will do the calcutation of protein surfaces based on X-ray data (PDB etc). I need sas and conolly-surfaces or other algorithms. I should -of course- be fast, easy to use, free (or cost almost nothing) etc. etc. and run on DOS or WINDOWS. thanks. andreas e-mail: aw1@chclu.chemie.uni-konstanz.de From owner-software@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!rutgers!gatech!swrinde!pipex!bnr.co.uk!corpgate!brtph500.bnr.ca!bcarh189.bnr.ca!nott!nrcnet0.nrc.ca!cansnd!jmau From: jmau@cansnd.cisti.nrc.ca (J. Mau) Newsgroups: bionet.software Subject: ATLAS on SGI Irix 5.2? Date: 6 Mar 1995 22:12:39 GMT Organization: National Research Council, Canada Lines: 16 Message-ID: <3jg1cn$2g4@nrcnet0.nrc.ca> NNTP-Posting-Host: cansnd.cisti.nrc.ca X-Newsreader: TIN [version 1.2 PL2] Hello: Has anyone been able to get the December 1994 release of ATLAS to work under Irix 5.2? It looks so simple, but I have been unable to get it to work. Thanks for any assistance. Jonathan --------------------------------------------------------------------- Jonathan Mau Phone (613)990-6248 Room 40 Bldg M-55 FAX (613)952-8246 NRC-CISTI jmau@cansnd.cisti.nrc.ca Ottawa, Ontario jemau@cisti.lan.nrc.ca K1A 0R6 From owner-software@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!uunet!boulder!tali.hsc.colorado.edu!NewsWatcher!user From: ikled@njc.org (David Ikle) Newsgroups: bionet.software Subject: Re: stats program Date: 6 Mar 1995 22:33:28 GMT Organization: National Jewish Hospital Lines: 22 Message-ID: References: <3j0jvg$iev@nnrp.ucs.ubc.ca> NNTP-Posting-Host: 198.243.65.4 In article <3j0jvg$iev@nnrp.ucs.ubc.ca>, stobbs@unixg.ubc.ca (Kathleen Stobbs) wrote: > Can anyone recommend a good stats program for use on the Mac for > scientific data analysis. I currently use StatView 4.0 but is doesn't > seem to accept data from Excel 5. Thanks for any and all advice. > > -- > Kathleen Stobbs > Dept. Obstetrics and Gynecology > University of British Columbia I highly recommend JMP, written by folks at SAS. Info and demo at http://www.sas.com -- David N. Ikle, Ph.D., Director Biostatistics and Academic Computing National Jewish Hospital Denver, CO 80206 ikled@njc.org From owner-software@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!news.ksu.ksu.edu!nbc.ksu.ksu.edu!not-for-mail From: dsb1763@ksu.ksu.edu (Echinococcus) Newsgroups: bionet.software Subject: sequencing programs Date: 6 Mar 1995 22:05:32 -0600 Organization: Kansas State University Lines: 4 Message-ID: <3jgm2c$dbg@nbc.ksu.ksu.edu> NNTP-Posting-Host: nbc.ksu.ksu.edu Summary: sequencing software X-Newsreader: NN version 6.5.0 #1 (NOV) ould someone tell if there is a shareware/freeware program that would read a scan of a sequencing gel radioautogram. Thank you to everyone who answered in advanced. My email address is dsb1763@ksu.ksu.edu P.S. I use a Macintosh, please responed with programs that will run on this platform. From owner-software@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.nysernet.net!news.sprintlink.net!howland.reston.ans.net!gatech!willis.cis.uab.edu!news.ecn.bgu.edu!newspump.wustl.edu!cerberus-138.wustl.edu!usenet From: HAVILAND@KIDS.WUSTL.EDU (David L. Haviland, Ph.D.) Newsgroups: bionet.software Subject: Re: Bibliography software Date: 7 Mar 1995 18:42:49 GMT Organization: Washington University School of Med. Lines: 46 Distribution: world Message-ID: <3ji9f9$o2i@cerberus-138.wustl.edu> References: <3j4epv$s3a@hermod.uio.no> NNTP-Posting-Host: kids3.wustl.edu X-News-Reader: VMS NEWS v1.25 In-Reply-To: thomas.hansteen@bio.uio.no's message of 2 Mar 1995 12:47:59 GMT In <3j4epv$s3a@hermod.uio.no> thomas.hansteen@bio.uio.no writes: > > We want to collect our litterature databases, who currently are in EndNote-, ProCite- and > PopLitt-formats, into one, Word 6.0 (Windows)-compatible Bibliography database. > The main qualities we are looking for is import/export routines and friendlyness. > > Any suggestions? > (I have seen above that EndNote for windows, my favorite, is in a > prenatal commercial fase, > what a pity.) Thomas: Sure, I'll bite... and those that scan this sub know what I'm going to say... ;-) I would opt for Papyrus. For $99 it does what you ask. No extra costs, no extra modules, no nothin'... It comes ready with a variety of formats for both imports and exports - you can easily design both to suit your needs. Here at Wash-U we have a library format that didn't quite match what came with Papyrus, I had a import format up and working within about a hour. Currently, it is available in DOS format. The DOS format works fine under Windows (personal experience) and a Mac version is currently under development. Dave Goldman who deveoped it (and sells it) can be reached at: rsd@teleport.com Hope this helps. David (blah-blah - no affiliation with RSD) =========================================================================== + David L. Haviland, Ph.D. Internet:"haviland@kids.wustl.edu" + + Washington Univ. School of Med. A.K.A : The Compiler + + Dept. of Peds./Pulm. Box 8116 ICBM-Net : Just hit St. Louis + + 400 S. Kingshighway &-6 <- User is Brain Dead... + + St. Louis, MO 63110 FAX: 314-454-2476 + + (314) 454-6076 + + ------------------------------------------------------------------- + + Outside of a cat, a book is a man's best friend. Inside of a cat, + + it's too dark to read! + =========================================================================== From owner-software@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.nysernet.net!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.software Subject: EMBL/Genbank crossrefs Date: 7 Mar 1995 16:47:10 -0000 Lines: 29 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3ji2me$cnn@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk Dear colleagues, A friend of mine gave me a list of 300 Genbank IDs (IDs, NOT accession numbers). I'd like to process these sequences. But here we have EMBL, not Genbank. And since the IDs are different..... Is there a simple way to make the links between EMBL and Genbank IDs, or to retrieve the accession numbers of the 300 sequences from their IDs? I don't feel like using W3SRS in a server and retrieving manually, one by one, the 300 accession numbers.... Thanks for your help, Jean-Loup --------------------------------------------------------------------- Jean-Loup Risler Tel: (33 1) 69 82 31 34 CNRS Fax: (33 1) 69 07 49 73 Centre de Genetique Moleculaire Email: risler@cgmvax.cgm.cnrs-gif.fr 91198 Gif sur Yvette Cedex France --------------------------------------------------------------------- From owner-software@net.bio.net Mon Mar 06 22:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!lll-winken.llnl.gov!noc.near.net!saturn.caps.maine.edu!jax!news From: Carolyn Blake Subject: vial label printer Message-ID: <1995Mar7.132119.12969@jax.org> Sender: news@jax.org Nntp-Posting-Host: emanon Organization: The Jackson Laboratory, Bar Harbor, ME 04609 Date: Tue, 7 Mar 95 13:21:19 GMT Lines: 6 I'm looking for a printer that will print 1/4" round labels for vial tops in the lab. Any pointers or experiences would be greatly appreciated! thanks cb From owner-software@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!ee.und.ac.za!ucthpx!itu1.sun.ac.za!k4027.mikro.SUN.AC.ZA!Marco From: Marco@MATIES.SUN.AC.ZA (Marco Gagiano ) Newsgroups: bionet.software Subject: PROSAII Date: Tue, 7 Mar 1995 06:22:32 GMT Organization: MICROBIOLOGY Lines: 6 Message-ID: NNTP-Posting-Host: 146.232.84.17 X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #4] I am looking for the FTP-site for the PROSAII package. It was apparently posted here some time ago. Any help will be greatly appreciated. Thanks. Marco Gagiano From owner-software@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!newsjunkie.ans.net!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: instigase@aol.com (Instigase) Newsgroups: bionet.software Subject: Re: Fitting program for thermodynamic parameters needed ! Date: 6 Mar 1995 23:17:54 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 12 Sender: root@newsbf02.news.aol.com Message-ID: <3jgmpi$erl@newsbf02.news.aol.com> References: Reply-To: instigase@aol.com (Instigase) NNTP-Posting-Host: newsbf02.mail.aol.com Check out the program BIOEQS its freeware from the author, its user-unfriendly but powerful. Read the article by the author: Royer, Catherine A., Anal Biochem, (1993), 210:91-97 "Improvements in the Numerical Analysis of Thermodynamic Data from Biomolecular Complexes." good luck Lou Reynaldo Penn State University From owner-software@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.nysernet.net!news.sprintlink.net!howland.reston.ans.net!gatech!asuvax!noao!math.arizona.edu!news.Arizona.EDU!dank From: dank@river.hwr.arizona.edu (Dan Braithwaite) Newsgroups: bionet.software Subject: wanted: MSwin app for multi-alignment of seqs Date: 6 Mar 1995 19:39:25 GMT Organization: uofa hwr Lines: 32 Message-ID: <3jfodd$tvu@news.ccit.arizona.edu> NNTP-Posting-Host: river.hwr.arizona.edu Originator: dank@river.hwr.arizona.edu Hello, I recently bought myself a PC and would like to be able to do some work at home without running GCG over the modem. I spent some time looking around the various ftp sites I could find for an MSwindows application that will allow me to easily align over 50 sequences at once. To no avail. What do people use on the PC as a standalone program for sequence alignment? GCG is my package of choice and I am not interested in laying out any large amounts of money for a big PC package that might do the alignment work plus umpteen other things I don't particularly need. I have used GDE for Xwindows and find it to be fairly good, but I will settle for any crude app for MSwindows no need for any extras like computer alignment routines, distance matrix calculations, or tree making functions. Is it possible to use a spreadsheet for this business? Any and all insight suggestions etc. appreciated. Thanks, -- dan braithwaite, email: dank@hwr.arizona.edu computer programmer, Dept. of Hydrology & Dept. of Microbiology and Immunology, College of Medicine University of Arizona Ph: (602) 621-9944, Fax: (602) 621-1422 From owner-software@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!mtool.com!lincoln From: lincoln@mtool.com (Steve Lincoln) Newsgroups: bionet.software Subject: Re: Re: Linux version of Mapmaker Date: 6 Mar 1995 06:35:46 -0800 Organization: Molecular Tool, Inc. Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <3000954877.325609957@mtifc.mtool.com> Reply-To: lincoln@mtool.com There is a DOS version already available (compiled with WATCOM C/386) which uses virtual memory and runs pretty big problems. The linux port should be no harder than any other Unix port, but if someone has done it I don't know about it. The source and the DOS binaries can be found on genome.wi.mit.edu and multiple other places on the net. - SL From owner-software@net.bio.net Mon Mar 06 22:00:00 1995 Newsgroups: bionet.software Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!news From: ewan birney Subject: Re: nucleic acid binding domains Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Tue, 7 Mar 1995 20:15:41 GMT References: Organization: European Bioinformatics Institute Lines: 57 Newswatcher@sickkids.on.ca (Newswatcher) wrote: > > Could anyone suggest a database/software where upon entering the AA > sequence, possible DNA/RNA binding domains cou