From owner-software@net.bio.net Sun Aug 01 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!sol.ctr.columbia.edu!xlink.net!news.dfn.de!news.uni-bielefeld.de!nowhere!hsunsrv!schneide From: schneide@wi-inf.uni-essen.de (Axel Schneider) Newsgroups: bionet.software Subject: Help wanted for THESIS in mobile computer communication Message-ID: Date: 2 Aug 93 13:33:06 GMT Sender: newsadm@uni-essen.de Reply-To: schneide@wi-inf.uni-essen.de Organization: Wirtschaftsinformatik Universitaet Essen Lines: 17 Nntp-Posting-Host: wi-inf.uni-essen.de I am seeking assistance for my university thesis, which will look at opportunities for using mobile computer communication to aid the environment. I would be grateful for any information supplied or suggestions for obtaining information, as books on this topic are scarce. I have outlined below the areas of interest for me, pertaining to this subject. 1) Any existing cases if computers helping to improve or monitor the environment. 2) Detailed and technical information on mobile computer communication. 3) The protection of privacy using mobile computer communication. 4) Any details of the USENIX Mobile and Location-Independant Computing Symposium to be held in August this year in Massachusetts, USA, and the eMail-Adress of USENIX in Berkeley, California. I hope your suggestions and information will make my thesis a success. I look forward to hearing from you all soon. Thanks in advance Axel Schneider PS: Please send eMail to: schneide@wi-inf.uni-essen.de From owner-software@net.bio.net Sun Aug 01 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!not-for-mail From: jckelley@tigr.org (John C. Kelley) Newsgroups: bionet.software Subject: PIR weirdness Message-ID: <9308021205.AA26976@bengal.tigr.org> Date: 2 Aug 93 12:00:55 GMT Sender: daemon@cs.utexas.edu Organization: UTexas Mail-to-News Gateway Lines: 35 NNTP-Posting-Host: cs.utexas.edu NetGreetings, We have just noticed a peculiarity in PIR Release 36 that I hope someone can explain (and tell me it hasn't been there too long, since I haven't noticed it earlier...). See below: SEQUENCE 5 10 15 20 25 30 1 G D V E K G K K I F(V,Q.K.C.A.Q.C.H.T.C,E.K.G.G.K.H)K V G P 31 N L Y G L I G R K T G Q A A G F S Y T D A N K N K G I T W(G. 61 E,D,T.L.M.E.Y)L E N P K K Y I P G T K M I F A G I(K.K.K.G.E. 91 R.Q)D L I A Y(L.K.S,A,C,S,K) /// This is the sequence from entry A00021. What I am curious about is the portions surrounded by parens whose proteins are seperated by commas or periods. At first thought, this seems to indicate that these proteins are uncertain, that it could any one in the list. This doesn't bear out however since some commercial releases of this entry simply strip the extraneous characters out leaving the sequence as is. THe only other thing I can think is that this is pointing out some artifact of this part of the sequence. Could someone please enlighten me as to the meaning of this sequence notation? Thanks John Kelley ---- John C. Kelley jckelley@tigr.org Computer Systems Manager (301) 869-9056 The Institute for Genomic Research 932 Clopper Road Gaithersburg, MD 20878 From owner-software@net.bio.net Sun Aug 01 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!Germany.EU.net!mcsun!dkuug!uts!biobase!pamaga From: pamaga@biobase.aau.dk (Paulo Magalhaes) Newsgroups: bionet.software Subject: Re: Image analysis software Message-ID: Date: 2 Aug 93 07:57:11 GMT References: <23744p$25q@ausom.ausom.oz.au> Organization: The Danish BioBase Lines: 8 Daniel M Goldman writes: >For those interested in image analysis, I suggest you subscribe to >"Advanced Imaging" and watch for developments and ads for equipment/ >software. If you can't get the address from your library, contact me >and I will post it. -DmG Yes, please. From owner-software@net.bio.net Sun Aug 01 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!emba-news.uvm.edu!brianf From: brianf@med.uvm.edu (Brain Foley) Newsgroups: bionet.software Subject: Re: PDB - GCG or GENBANK accession number tables Message-ID: <1993Aug2.150440.26409@emba.uvm.edu> Date: 2 Aug 93 15:04:40 GMT References: <1993Jul30.152722.27301@gserv1.dl.ac.uk> Sender: news@emba.uvm.edu Distribution: bionet Organization: University of Vermont -- Division of EMBA Computer Facility Lines: 14 X-Newsreader: TIN [version 1.2 PL1] bionet@FRCGM51.EARN wrote: : : In brief: I'm a VERY happy user of SRS.... : : -------------------------------------------------------------------- : | Jean-Loup Risler | | : | CNRS | risler@frcgm51.bitnet | : | Centre de Genetique Moleculaire | risler@cgmvax.cgm.cnrs-gif.fr | : | 91198 Gif sur Yvette Cedex France | | : -------------------------------------------------------------------- : Sounds great! Where can I get SRS and what systems will it run on? From owner-software@net.bio.net Sun Aug 01 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!emba-news.uvm.edu!brianf From: brianf@med.uvm.edu (Brain Foley) Newsgroups: bionet.software,bionet.molbio.pir Subject: Re: PIR weirdness Message-ID: <1993Aug2.151911.26679@emba.uvm.edu> Date: 2 Aug 93 15:19:11 GMT References: <9308021205.AA26976@bengal.tigr.org> <1993Aug2.144542.11508@cs.wisc.edu> Sender: news@emba.uvm.edu Organization: University of Vermont -- Division of EMBA Computer Facility Lines: 63 Xref: biosci bionet.software:5573 X-Newsreader: TIN [version 1.2 PL1] Scott Rose (rose@galtee.cs.wisc.edu) wrote: : In article <9308021205.AA26976@bengal.tigr.org> jckelley@tigr.org (John C. Kelley) writes: : > We have just noticed a peculiarity in PIR Release 36 that I hope : >someone can explain (and tell me it hasn't been there too long, since I : >haven't noticed it earlier...). See below: : > : >SEQUENCE : > 5 10 15 20 25 30 : > 1 G D V E K G K K I F(V,Q.K.C.A.Q.C.H.T.C,E.K.G.G.K.H)K V G P : > 31 N L Y G L I G R K T G Q A A G F S Y T D A N K N K G I T W(G. : > 61 E,D,T.L.M.E.Y)L E N P K K Y I P G T K M I F A G I(K.K.K.G.E. : > 91 R.Q)D L I A Y(L.K.S,A,C,S,K) : >/// : > : >This is the sequence from entry A00021. What I am curious about is : >the portions surrounded by parens whose proteins are seperated by : >commas or periods. At first thought, this seems to indicate that : >these proteins are uncertain, that it could any one in the list. : >This doesn't bear out however since some commercial releases of : >this entry simply strip the extraneous characters out leaving the : >sequence as is. THe only other thing I can think is that this is : >pointing out some artifact of this part of the sequence. : > : >Could someone please enlighten me as to the meaning of this sequence : >notation? : Perhaps this documentation that I found squirreled away will help. : No offense to squirrels intended, and I can't say with certainty : where this came from: : Punctuation in Protein Sequences : Two adjacent amino acids, with no punctuation or with a blank : between, indicates that they are connected, as determined : experimentally. : () Encloses a region, the composition but not the complete : sequence of which has been determined experimentally, or : encloses a single residue that has been tentatively : identified. : = Indicates )(, the juxtaposition of two regions of : indeterminate sequence, while preserving proper spacing : between amino acids. : / Indicates that the adjacent amino acids are from different : peptides, not necessarily connected. When the amino end of a : protein has not been determined, / precedes the first : residue. When the carboxyl end has not been determined, / : follows the last residue. When )/, /(, or )/( are needed, : only / is used. : . Outside of parentheses, indicates the ends of sequenced : fragments. The relative order of these fragments was not : determined experimentally but is clear from homology or other : indirect evidence. : . Within parentheses, indicates that the amino acid to its left : has been placed with at least 90% confidence by homology with : known sequences. : , Indicates that the amino acid to its left could not be : positioned with confidence by homology. I am just cross-posting this to BIONET.MOLBIO.PIR in case someone in the future looks in the archives of that list for info on PIR notations. They may not think to look in the archives of this group for PIR info. From owner-software@net.bio.net Sun Aug 01 23:00:00 1993 Path: biosci!uwm.edu!daffy!uwvax!galtee.cs.wisc.edu!rose From: rose@galtee.cs.wisc.edu (Scott Rose) Newsgroups: bionet.software Subject: Re: PIR weirdness Message-ID: <1993Aug2.144542.11508@cs.wisc.edu> Date: 2 Aug 93 14:45:42 GMT References: <9308021205.AA26976@bengal.tigr.org> Sender: news@cs.wisc.edu (The News) Organization: University of Wisconsin, Madison -- Computer Sciences Dept. Lines: 57 In article <9308021205.AA26976@bengal.tigr.org> jckelley@tigr.org (John C. Kelley) writes: > We have just noticed a peculiarity in PIR Release 36 that I hope >someone can explain (and tell me it hasn't been there too long, since I >haven't noticed it earlier...). See below: > >SEQUENCE > 5 10 15 20 25 30 > 1 G D V E K G K K I F(V,Q.K.C.A.Q.C.H.T.C,E.K.G.G.K.H)K V G P > 31 N L Y G L I G R K T G Q A A G F S Y T D A N K N K G I T W(G. > 61 E,D,T.L.M.E.Y)L E N P K K Y I P G T K M I F A G I(K.K.K.G.E. > 91 R.Q)D L I A Y(L.K.S,A,C,S,K) >/// > >This is the sequence from entry A00021. What I am curious about is >the portions surrounded by parens whose proteins are seperated by >commas or periods. At first thought, this seems to indicate that >these proteins are uncertain, that it could any one in the list. >This doesn't bear out however since some commercial releases of >this entry simply strip the extraneous characters out leaving the >sequence as is. THe only other thing I can think is that this is >pointing out some artifact of this part of the sequence. > >Could someone please enlighten me as to the meaning of this sequence >notation? Perhaps this documentation that I found squirreled away will help. No offense to squirrels intended, and I can't say with certainty where this came from: Punctuation in Protein Sequences Two adjacent amino acids, with no punctuation or with a blank between, indicates that they are connected, as determined experimentally. () Encloses a region, the composition but not the complete sequence of which has been determined experimentally, or encloses a single residue that has been tentatively identified. = Indicates )(, the juxtaposition of two regions of indeterminate sequence, while preserving proper spacing between amino acids. / Indicates that the adjacent amino acids are from different peptides, not necessarily connected. When the amino end of a protein has not been determined, / precedes the first residue. When the carboxyl end has not been determined, / follows the last residue. When )/, /(, or )/( are needed, only / is used. . Outside of parentheses, indicates the ends of sequenced fragments. The relative order of these fragments was not determined experimentally but is clear from homology or other indirect evidence. . Within parentheses, indicates that the amino acid to its left has been placed with at least 90% confidence by homology with known sequences. , Indicates that the amino acid to its left could not be positioned with confidence by homology. From owner-software@net.bio.net Sun Aug 01 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!uknet!pipex!uunet!spool.mu.edu!uwm.edu!msuinfo!netnews.upenn.edu!hmivax!bailey From: bailey@genetics.upenn.edu (Charles Bailey) Newsgroups: bionet.software Subject: Re: PDB - GCG or GENBANK accession number tables Message-ID: <1993Aug2.153948.1@hmivax.humgen.upenn.edu> Date: 2 Aug 93 19:39:48 GMT References: <1993Jul30.152722.27301@gserv1.dl.ac.uk> <1993Aug2.150440.26409@emba.uvm.edu> Sender: news@netnews.upenn.edu Distribution: bionet Organization: HHMI/Human Genetics, Univ of Pa. Lines: 23 Nntp-Posting-Host: hmivax.humgen.upenn.edu In article <1993Aug2.150440.26409@emba.uvm.edu>, brianf@med.uvm.edu (Brain Foley) writes: > Sounds great! Where can I get SRS and what systems will it run > on? You can pick it up in North America from genetics.upenn.edu by anonymous ftp, in the directory Anon_Root:[Bio.SRS]. This is a mirror of the official distribution site in Europe, biomed.uio.no. SRS will run under VMS, and I'm not aware of any hardware restrictions. As a performance issue, it likes a lot of virtual memory and will consume a lot of cycles building its indices, but lookups by users are no real strain on memory or CPU. I hope this helps. If I can help further, please don't hesitate to drop me a line. Good luck. Regards, Charles Bailey !------------------------------------------------------------------------------- ! Dept. of Genetics / Howard Hughes Medical Institute ! University of Pennsylvania School of Medicine Rm. 430 Clinical Research Bldg. ! 422 Curie Blvd. Philadelphia, PA 19104 USA Tel. (215) 898-1699 ! Internet: bailey@genetics.upenn.edu (IN 128.91.200.37) !------------------------------------------------------------------------------- From owner-software@net.bio.net Mon Aug 02 23:00:00 1993 Path: biosci!parc!decwrl!ames!elroy.jpl.nasa.gov!usc!cs.utexas.edu!uunet!math.fu-berlin.de!cs.tu-berlin.de!mailgzrz.TU-Berlin.DE!news.dfn.de!immunbio.mpg.de!immunbio.mpg.de!news From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Newsgroups: bionet.software Subject: Re: PDB - GCG or GENBANK accession number tables Message-ID: <1993Aug2.235543.39@immunbio.mpg.de> Date: 2 Aug 93 22:55:43 GMT References: <1993Jul30.152722.27301@gserv1.dl.ac.uk> <1993Aug2.150440.26409@emba.uvm.edu> Organization: Max-Planck-Institut fuer Immunbiologie Lines: 36 Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24In-Reply-To: brianf@med.uvm.edu's message of Mon, 2 Aug 1993 15:04:40 GMTLines: 36 In <1993Aug2.150440.26409@emba.uvm.edu> brianf@med.uvm.edu writes: > bionet@FRCGM51.EARN wrote: > > : > : In brief: I'm a VERY happy user of SRS.... > : > Sounds great! Where can I get SRS and what systems will it run > on? SRS is available via anonymous FTP from the Norwegian EMBnet node: biomed.uio.no It runs on VMS platforms. As far as I know there is a beta version for UNIX but I don't know the exact status. Contact the developer of SRS, Thure Etzold, at EMBL: etzold@embl-heidelberg.de about the UNIX version. Regards Christoph Gartmann +----------------------------------------------------------------------------+ | Christoph Gartmann Phone : +49-761-5108-465 Fax: -221 | | Max-Planck-Institut fuer PSI : PSI%(0262)45050160374::GARTMANN | | Immunbiologie Internet: gartmann@immunbio.mpg.de | | Postach 1169 | | D-79011 Freiburg, FRG | +------------- Do you know MENUE, the user environment for VMS? -------------+ +----------------------------------------------------------------------------+ | Christoph Gartmann Phone : +49-761-5108-465 Fax: -221 | | Max-Planck-Institut fuer PSI : PSI%(0262)45050160374::GARTMANN | | Immunbiologie Internet: gartmann@immunbio.mpg.de | | Postach 1169 | | D-79011 Freiburg, FRG | +------------- Do you know MENUE, the user environment for VMS? -------------+ From owner-software@net.bio.net Mon Aug 02 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!spool.mu.edu!uwm.edu!daffy!uwvax!galtee.cs.wisc.edu!rose From: rose@galtee.cs.wisc.edu (Scott Rose) Newsgroups: bionet.software Subject: Re: PDB - GCG or GENBANK accession number tables Message-ID: <1993Aug3.030806.20977@cs.wisc.edu> Date: 3 Aug 93 03:08:06 GMT References: <1993Jul30.152722.27301@gserv1.dl.ac.uk> <1993Aug2.150440.26409@emba.uvm.edu> <1993Aug2.153948.1@hmivax.humgen.upenn.edu> Sender: news@cs.wisc.edu (The News) Distribution: bionet Organization: University of Wisconsin, Madison -- Computer Sciences Dept. Lines: 25 In article <1993Aug2.153948.1@hmivax.humgen.upenn.edu> bailey@genetics.upenn.edu (Charles Bailey) writes: >In article <1993Aug2.150440.26409@emba.uvm.edu>, brianf@med.uvm.edu (Brain Foley) writes: >> Sounds great! Where can I get SRS and what systems will it run >> on? > >You can pick it up in North America from genetics.upenn.edu by anonymous ftp, >in the directory Anon_Root:[Bio.SRS]. This is a mirror of the official >distribution site in Europe, biomed.uio.no. SRS will run under VMS, and I'm >not aware of any hardware restrictions. As a performance issue, it likes a lot >of virtual memory and will consume a lot of cycles building its indices, but >lookups by users are no real strain on memory or CPU. Just a couple of addendums (addenda?) to that-- the indices are large and will consume lots of disk space, more than proportional to the size of your installed data because of links between databases. Disk is cheap these days, though. Also, SRS is appearing on Unix these days-- it's known to run on Ultrix, Irix, and various flavors of SunOS. I can't say for sure that it has actually been released for those platforms, but I didn't want it to go unsaid that the work has been done and the availability of the product for Unix is at the least imminant. Conveniently, common sources are used to build on all platforms. -S From owner-software@net.bio.net Mon Aug 02 23:00:00 1993 Path: biosci!BDT.FTPT.BR!adriano From: adriano@BDT.FTPT.BR (Adriano Cesar da Silva) Newsgroups: bionet.software Subject: PROLE III Message-ID: <9308031428.AA08309@sabia.ftpt.br> Date: 3 Aug 93 11:28:12 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 28 Dear everybody I would like to know that you know a software: PROLE III: A Computer Program for Yeast Identification and for Teaching Yeast Systematics Author : E.Monte, E.Velazquez, P.Mateos and A.Chordi Departament of Microbiology, Genetic University of Salamanca - SPAIN If you know, can you tell me how I can contact us, address, e-mail or another information! Please, execuse me, my english is bad Thank you, for you attention Adriano. -- ```` (o o) |----------------------oOO---(__)---OOo----------------------| | | | Adriano Cesar da Silva adriano@bdt.ftpt.br | | Fundacao "Andre Tosello" tel: +55 192 42 7022 | | Base de Dados Tropical - BDT fax: +55 192 42 7827 | | Campinas - Sao Paulo Brasil | |------------------------------------------------------------| || || () () From owner-software@net.bio.net Mon Aug 02 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.software Subject: SRS features (Re: PDB - GCG or GENBANK accession number tables) Message-ID: <1993Aug3.063533.23853@comp.bioz.unibas.ch> Date: 3 Aug 93 06:35:33 GMT References: <1993Jul30.152722.27301@gserv1.dl.ac.uk> <1993Aug2.150440.26409@emba.uvm.edu> <1993Aug2.153948.1@hmivax.humgen.upenn.edu> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Distribution: bionet Organization: EMBnet Switzerland [BASEL] Lines: 77 Nntp-Posting-Host: biox.embnet.unibas.ch In article <1993Aug2.153948.1@hmivax.humgen.upenn.edu>, bailey@genetics.upenn.edu (Charles Bailey) writes: |> In article <1993Aug2.150440.26409@emba.uvm.edu>, brianf@med.uvm.edu (Brain Foley) writes: |> > Sounds great! Where can I get SRS and what systems will it run |> > on? |> |> You can pick it up in North America from genetics.upenn.edu by anonymous ftp, |> in the directory Anon_Root:[Bio.SRS]. This is a mirror of the official |> distribution site in Europe, biomed.uio.no. SRS will run under VMS, and I'm We (Dr. Lukas Rosenthaler and myself) ported SRS 3.0 to UNIX earlier this year. After some testing (which revealed quite a few problems) we communicated the source code back to Thure Etzold, who is the author of SRS. At the time we had the code, it worked fine on IRIX, ULTRIX, SUNOS. We run it on OpenVMS (currently, not yet on the AXP) also. You might want to ask Thure Etzold (etzold@embl-heidelberg.de) for details on which platforms the next release will run on, and whether you would volunteer to test it :-) . The (possible) restriction I can see is disk space. SRS indexes a lot of fields in the database, and relies heavily on SWISSPROT DR records. The crosslinks consume a bit of a disk space (on a VMS cluster): Directory SRS$ROOT2:[SRS_INDEX] Total of 229 files, 237309/237740 blocks. This is for most of the available sequence databases today, including a few additional ones: 'yogi > dir biobig:[biozen.data...]/grand/size=all Grand total of 18 directories, 796 files, 1792246/1793736 blocks. so this is about 15% of total. Just sequence data (e.g., GCG) stuff is smaller, however; $ dir biobig:[biozen.data...]*.ref, biobig:[biozen.data...]*.seq, - biobig:[biozen.data...]*.names, biobig:[biozen.data...]*.numbers, - biobig:[biozen.data...]*.seqcat/grand/size=all Grand total of 41 directories, 205 files, 1158655/1158992 blocks. On UNIX, it is similar (sizes in blocks, on a Silicon Graphics Cluster); 268739 /biox/biocomputing/srs/data 1338000 /bioy/data/ which means that you will come up with a proportion of 25% of the already occupied disk space However, disk space is not that short any longer. Remember that SRS can use more than the plain sequence data sets, such as PDB, PROSITE, and many more. There are other indexing systems on the market, e.g., WAIS. If I run du on my WAIS'ed EMBL: 115246 /bioy/gopher-data/index/embl then this is only about a third, BUT only for EMBL, and not with any links, and not specific fields, and and and... I could continue the listing with other examples on other program packages. You must be aware that the added performance and functionality has to be paid for with something. Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ftp mirror at nic.switch.ch ----------------------------------------- From owner-software@net.bio.net Mon Aug 02 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!darwin.sura.net!news.dfn.de!immunbio.mpg.de!immunbio.mpg.de!news From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Newsgroups: bionet.software Subject: Re: SRS features (Re: PDB - GCG or GENBANK accession Message-ID: <1993Aug4.004010.40@immunbio.mpg.de> Date: 3 Aug 93 23:40:10 GMT References: <1993Jul30.152722.27301@gserv1.dl.ac.uk> <1993Aug2.150440.26409@emba.uvm.edu> <1993Aug2.153948.1@hmivax.humgen.upenn.edu> <1993Aug3.063533.23853@comp.bioz.unibas.ch> Organization: Max-Planck-Institut fuer Immunbiologie Lines: 25 Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24In-Reply-To: doelz@comp.bioz.unibas.ch's message of Tue, 3 Aug 1993 06:35:33 GMTLines: 25 Just a small amendement to Reinhard Doelz's post: SRS may be tailored just to create only the indices and links for the data and fields you would like to have indexed. This may reduce disk space. But of course, the more fields are indexed and the more links you have, the more powerful SRS is. Regards Christoph Gartmann +----------------------------------------------------------------------------+ | Christoph Gartmann Phone : +49-761-5108-465 Fax: -221 | | Max-Planck-Institut fuer PSI : PSI%(0262)45050160374::GARTMANN | | Immunbiologie Internet: gartmann@immunbio.mpg.de | | Postach 1169 | | D-79011 Freiburg, FRG | +------------- Do you know MENUE, the user environment for VMS? -------------+ +----------------------------------------------------------------------------+ | Christoph Gartmann Phone : +49-761-5108-465 Fax: -221 | | Max-Planck-Institut fuer PSI : PSI%(0262)45050160374::GARTMANN | | Immunbiologie Internet: gartmann@immunbio.mpg.de | | Postach 1169 | | D-79011 Freiburg, FRG | +------------- Do you know MENUE, the user environment for VMS? -------------+ From owner-software@net.bio.net Mon Aug 02 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!isgate!krafla!php From: php@rhi.hi.is (Petur Henry Petersen) Newsgroups: bionet.software Subject: need dna editor for unix Message-ID: <7408@krafla.rhi.hi.is> Date: 3 Aug 93 17:19:44 GMT Sender: usenet@rhi.hi.is Lines: 10 Nntp-Posting-Host: hengill.rhi.hi.is Well the title says it all. I need some kind of software that runs under UNIX which allows me to make comparisons and translate DNA into protein. Just email me... ThanX p.henry Deptm.bioloy u.Iceland ps: Where is the faq for this group? From owner-software@net.bio.net Mon Aug 02 23:00:00 1993 Path: biosci!uwm.edu!daffy!uwvax!galtee.cs.wisc.edu!rose From: rose@galtee.cs.wisc.edu (Scott Rose) Newsgroups: bionet.software Subject: Re: PDB - GCG or GENBANK accession number tables Message-ID: <1993Aug3.144640.21046@cs.wisc.edu> Date: 3 Aug 93 14:46:40 GMT References: <1993Jul30.152722.27301@gserv1.dl.ac.uk> <1993Aug2.150440.26409@emba.uvm.edu> <1993Aug2.235543.39@immunbio.mpg.de> Sender: news@cs.wisc.edu (The News) Organization: University of Wisconsin, Madison -- Computer Sciences Dept. Lines: 12 In article <1993Aug2.235543.39@immunbio.mpg.de> GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) writes: > Contact the developer of SRS, Thure Etzold, at EMBL: > etzold@embl-heidelberg.de about the UNIX version. A little bird told me that Dr. Etzold is on vacation for two weeks or so, in a place from which the answering of email is not possible. This same bird suggests that this information may be of solace to those who write to him and receive only silence in reply, at least until mid-August. -S From owner-software@net.bio.net Mon Aug 02 23:00:00 1993 Path: biosci!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!math.ohio-state.edu!cs.utexas.edu!uunet!destroyer!cs.ubc.ca!news.UVic.CA!ra.royalroads.ca!kkeen From: kkeen@post.RoyalRoads.ca (Kevin Keen) Newsgroups: bionet.software Subject: WANTED: Familial Data for a Quantitative Characteristic Keywords: Familial Correlation, Intraclass Correlation, Linkage Analysis Message-ID: <1993Aug3.224940.22938@ra.royalroads.ca> Date: 3 Aug 93 22:49:40 GMT Sender: kkeen@ra.royalroads.ca (Kevin Keen) Organization: Royal Roads Military College, Victoria, B.C. Lines: 26 1. Normally on bionet.software, messages are relayed concerning software. However, I would like to know if anyone has done a recent survey on human families or an breeding experiment with animal sibships. I'm finishing a methodology paper and a recent example with a quantitative characteristic is required. 2. Should you have such a data set; please contact the undersigned either by email, phone, or fax. 3. A new intraclass correlation (or sib-sib correlation) estimator is being proposed and must be compared with existing estimators. Monte Carlo simulations have shown the new estimator to be nearly as efficient as the maximum likelihood estimator without the need for iterative numerical solution. The ML estimate would be calculated for the data in addition to the other more popular estimates. Kevin J. Keen Maths Dept Royal Roads Military College FMO Victoria, BC, CANADA V0S 1B0 phone: 604/363-4590 fax: 604/363-4513 email: kkeen@tyr.royalroads.ca From owner-software@net.bio.net Tue Aug 03 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!uunet!noc.near.net!news.cs.brandeis.edu!NewsWatcher!user From: erman@brandeis.edu.bitnet (batu erman) Newsgroups: bionet.software Subject: looking for hyperblast Message-ID: Date: 4 Aug 93 16:34:45 GMT Sender: news@news.cs.brandeis.edu (USENET News System) Followup-To: bionet.software Organization: brandeis university Lines: 4 I am looking for a program called hyperblast to search genbank from a mac. Can someone please send me the address that I can ftp it from. thanks. Batu Erman From owner-software@net.bio.net Tue Aug 03 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!uunet!psinntp!phinet!tennant From: tennant@hau410.uk.smithkline.com (Mike Tennant) Newsgroups: bionet.software Subject: clustering algorithms Message-ID: <1993Aug4.093230.25768@netnews.smithkline.com> Date: 4 Aug 93 09:32:30 GMT Sender: news@netnews.smithkline.com (USENET News System) Organization: Smithkline Beecham Pharmaceuticals, Harlow, UK. Lines: 10 Hi all!, I'm looking for some software to perform clustering calculations on protein sequences, preferably not related to parsimony methods. Could anybody direct me to software which does this? -- cheers, Mike. From owner-software@net.bio.net Tue Aug 03 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!uunet!europa.eng.gtefsd.com!howland.reston.ans.net!torn!watserv2.uwaterloo.ca!CIVOFFICE.watstar.uwaterloo.ca!JRSETTI From: JRSETTI@CIVOFFICE.watstar.uwaterloo.ca (Jose R. Setti) Newsgroups: bionet.software Subject: Medical images in CD-ROM Message-ID: Date: 4 Aug 93 14:12:16 GMT Sender: news@watserv2.uwaterloo.ca Organization: University of Waterloo Lines: 10 I am sorry if this is not the best newsgroup for this question... I am asking this for a friend who is an ophtalmologist and wants to find where to buy a CD ROM with eye images. He read something on Newsweek. Does anyone know address of sellers of medical CD ROMs? Thanks in advance, -jrs ---jrs From owner-software@net.bio.net Tue Aug 03 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!math.ohio-state.edu!uwm.edu!msuinfo!netnews.upenn.edu!duong From: duong@chestnut.chem.upenn.edu (Duc Duong) Newsgroups: bionet.molbio.proteins,bionet.software,bionet.xtallography Subject: [HELP] Software calculte the angle between 2 planes? Message-ID: <139423@netnews.upenn.edu> Date: 4 Aug 93 17:57:19 GMT Sender: news@netnews.upenn.edu Followup-To: bionet.molbio.proteins Organization: NMR Biochemistry Graduate Research Lab Lines: 11 Xref: biosci bionet.molbio.proteins:786 bionet.software:5587 bionet.xtallography:391 Nntp-Posting-Host: chestnut.chem.upenn.edu hi.. I have 5 coordinates points that define 2 planes intersect each other. I'd like calculate the angle between them.. The problem is simple.. so is there any software would do this kind of calculation?? I don't want to re-invent the wheel here.. so can InsightII, Quanta?? etc.. do these kind of stuff.. The five angles have the x,y,z coordinates.. duc From owner-software@net.bio.net Tue Aug 03 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!uunet!europa.eng.gtefsd.com!darwin.sura.net!newt.welch.jhu.edu!welchdev.welch.jhu.edu!danj From: danj@welchdev.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.software Subject: Re: need dna editor for unix Message-ID: <1993Aug4.161239.29236@newt.welch.jhu.edu> Date: 4 Aug 93 16:12:39 GMT References: <7408@krafla.rhi.hi.is> Sender: news@newt.welch.jhu.edu Organization: Johns Hopkins University Genome Data Base (GDB) Lines: 66 Nntp-Posting-Host: welchdev.welch.jhu.edu In article <7408@krafla.rhi.hi.is> php@rhi.hi.is (Petur Henry Petersen) writes: > > Well the title says it all. I need some kind of software that runs >under UNIX which allows me to make comparisons and translate DNA into protein. >Just email me... ThanX > You might want to take a look at GDE (Genetic Data Envronment) - by Steve Smith. You can obtain GDE by gopher or anonymous ftp. Gopher sites: merlot.welch.jhu.edu, select: --> 3. FTP Sites, Software and Data Archives For Biology/ --> 22. GDE (Genetic Data Environment) (Harvard)/ megasun.BCH.UMontreal.CA, select: --> 5. GDE (The Genetic Data Environment)/ Anonymous ftp: golgi.harvard.edu in pub/GDE. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu And from the Readme file I snagged from Tim's site: ----------------------------------------------------------------------------- ...The GDE is a set of programs for multiple sequence alignment and analysis. The GDE currently runs on SUN SparcStations using OpenWindows 2.0 or MIT X11R4. The programs use an expandable user interface which allows the addition of external analysis functions without any rewriting of code. Analysis functions can be written in any language ('C',Fortran, Pascal Basic, shell scripts), and can be seamlessly merged into the systems menu/ dialog box interface. The system supports several data types, nucleic and amino acid sequences, text, and masking sequence, and three forms of color highlighting. The system can handle enormous alignments limited only by the amount of virtual memory on your workstation. Sequences can be edited under several levels of protection, as well as by aligned groups. The system has several external analysis functions included for such things as automated alignment, searching, homology recognition, and phylogenetic analysis. The programs are not in the public domain, but are and will continue to be available for free. Distribution includes full source code, and binaries along with a users manual. Steven Smith ---------------------------------------------------------------------------- From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.software Subject: Re: gcg package Message-ID: <1993Aug5.174529.15861@comp.bioz.unibas.ch> Date: 5 Aug 93 17:45:29 GMT References: <1993Aug5.111718.19595@gserv1.dl.ac.uk> <2033@alsys1.aecom.yu.edu> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 69 Nntp-Posting-Host: biox.embnet.unibas.ch In article <2033@alsys1.aecom.yu.edu>, zucker@leper1.ca.aecom.yu.edu (Thomas Zucker-Scharff x3513) writes: |> In article 19595@gserv1.dl.ac.uk, bss1jm@surrey.ac.uk (Dr Johnjoe Mcfadden) writes: ... |> >Does anybody know how much memory do we need to run the'gcg package' |> >from Genetics Computer Group Inc? ... |> I would suggest running GCG from a Sparcstation 10 with at least 48mb of ram, |> preferrably more. The pamphlet includes the following info: ... |> We are just switching over from the VMS version to the UNIX version on an SGI |> Challenge M series with 96mb of ram and 5gig of diskspace. It is basically irrelevant how much memory is _required_. It is the number of USERS and the number of jobs you want to run simultaneously which has to be accounted for. I personally run GCG on an AXP 4xxx (128 MB), a VAXCluster (7xxx (256 MB), 6xxx (64 MB)) and a Silicon Graphics UNIX Cluster (Crimson 64MB, and some Indigos down to 16MB). We have about 300 Users in the GCG accounting file, about 80 of them being 'power-users' using the system daily and several times a week. Disks are in the order of > 15 GB. As a rule of thumb, 8 MBytes of RAM and 50MB disk per head are a good start for a workgroup (5 to 20 people). If you run more users, think of per simultaneous _active_head in terms of RAM, but account for the same disk space. In the end, add at least 1 Gigabyte for scratch space and backup (if a disk crashes). To run all sequence databases you need about 8Gigabyte at the end of 1994 (might be wrong, but my schedule accounts for this). Big memory is needed for all programs which use virtual memory to access indices. This is not particularly a GCG feature, and will apply for most searching programs which use dynamic mempry allocation to larger extent. The 'QUICKSEARCH' program of GCG is a memory hog, and you will not necessarily want to run it. BLAST (from NCBI) certainly runs also much faster if you give it more memory to live in. Another valuable figure worth looking for is the I/O speed of the disk (sub)system and the caching options of the processor. Depending on the code, searches might become I/O bound. If you run off a small disk in PC-style fashion, your CPU might start idling and wastes time for I/O. Again, if you look at (whatever)-table oriented software ith will require some time to load the data, and the actual computation is a breeze. Do not seriously expect that you can run a cluster via NFS for sequence searching if you have only Ethernet. The workstations of today splatter 2 MBit/sec on a routine basis, and I managed to crash an ethernet with too many collissions and 8 workstations running FASTA accross the net. And, last not least, don't forget to order a batch system as well. UNIX might be great but usually does not come with a generic batch system. Unless you have very few users you might want to impose restrictions on the use of cpu-intensive software and send it to batch (can be easily achieved in most software, also at GCG). Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ftp mirror at nic.switch.ch ----------------------------------------- From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!europa.eng.gtefsd.com!darwin.sura.net!news-feed-2.peachnet.edu!umn.edu!csus.edu!netcom.com!netcomsv!nitelog!gartmann@immunbio.mpg.de From: gartmann@immunbio.mpg.de@nitelog.com (Gartmann@Immunbio.Mpg.De) Newsgroups: bionet.software Subject: Re: SRS features (Re: PDB - GCG or GENBANK accession Message-ID: <464.321.uupcb@nitelog.com> Date: 3 Aug 93 17:40:00 GMT References: <1993Jul30.152722.27301@gserv1.dl.ac.uk> Reply-To: gartmann@immunbio.mpg.de@nitelog.com (Gartmann@Immunbio.Mpg.De) Followup-To: ieee.general Organization: Nitelog BBS - Monterey, CA - 408-655-1096 Lines: 43 .@SUBJECT:Re: SRS features (Re: PDB - GCG or GENBANK accession Path: nuchat!menudo.uh.edu!swrinde!sdd.hp.com!math.ohio-state.edu darwin.sura.net!news.dfn.de!immunbio.mpg.de!immunbio.mpg.de!news Message-ID: <1993Aug4.004010.40@immunbio.mpg.de> From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Date: 4 Aug 93 00:40:10 +0100 <1993Aug2.150440.26409@emba.uvm.edu> <1993Aug2.153948.1@hmivax.humgen.upenn.edu> <1993Aug3.063533.23853@comp.bioz.unibas.ch> Organization: Max-Planck-Institut fuer Immunbiologie Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24In-Reply-To: doelz@comp.bioz.unibas.ch's message of Tue, 3 Aug 1993 06:35:33 GMTLines: 25 Lines: 25 Just a small amendement to Reinhard Doelz's post: SRS may be tailored just to create only the indices and links for the data and fields you would like to have indexed. This may reduce disk space. But of course, the more fields are indexed and the more links you have, the more powerful SRS is. Regards Christoph Gartmann +----------------------------------------------------------------------------+ | Christoph Gartmann Phone : +49-761-5108-465 Fax: -221 | | Max-Planck-Institut fuer PSI : PSI%(0262)45050160374::GARTMANN | | Immunbiologie Internet: gartmann@immunbio.mpg.de | | Postach 1169 | | D-79011 Freiburg, FRG | +------------- Do you know MENUE, the user environment for VMS? -------------+ +----------------------------------------------------------------------------+ | Christoph Gartmann Phone : +49-761-5108-465 Fax: -221 | | Max-Planck-Institut fuer PSI : PSI%(0262)45050160374::GARTMANN | | Immunbiologie Internet: gartmann@immunbio.mpg.de | | Postach 1169 | | D-79011 Freiburg, FRG | +------------- Do you know MENUE, the user environment for VMS? -------------+ --- . R109U:CLOUD9 From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!uunet!psinntp!alsys1!leper1!zucker From: zucker@leper1.ca.aecom.yu.edu (Thomas Zucker-Scharff x3513) Newsgroups: bionet.software Subject: Re: gcg package Message-ID: <2033@alsys1.aecom.yu.edu> Date: 5 Aug 93 14:51:37 GMT References: <1993Aug5.111718.19595@gserv1.dl.ac.uk> Sender: news@alsys1.aecom.yu.edu Reply-To: zucker@leper1.ca.aecom.yu.edu Lines: 40 Nntp-Posting-Host: leper1.ca.aecom.yu.edu In article 19595@gserv1.dl.ac.uk, bss1jm@surrey.ac.uk (Dr Johnjoe Mcfadden) writes: >We are considering buying a Sun Workstation to run molecular biology >software packages. > >Does anybody know how much memory do we need to run the'gcg package' >from Genetics Computer Group Inc? > >Thanks > >Johnjoe McFadden > >J.McFadden@uk.ac.surrey I believe GCG will email (or fax) you the information in their pamphlet, "Equipment Requirements For The Wisconsin Package". Email to beers@gcg.com. I would suggest running GCG from a Sparcstation 10 with at least 48mb of ram, preferrably more. The pamphlet includes the following info: Operating system: SunOS version 4.1.2 or 4.1.3 Software Required: Sun Fortran Compiler Version 1.4 Software Optional: OPEN LOOK (X Windows) Distribution Media: CD-ROM (ISO-9660) If you have tech questions, I've found Mike Hogan helpful (hogan@gcg.com). We are just switching over from the VMS version to the UNIX version on an SGI Challenge M series with 96mb of ram and 5gig of diskspace. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ | Tom Zucker-Scharff | | | Director Scientific Computing Facility | voice : 212-430-3512 | | Albert Einstein College of Medicine | beeper: 212-419-6984 | | 1300 Morris Park Avenue, Chanin 333 | fax : 212-822-6538 | | Bronx, New York 10461 USA | e-mail: zucker@aecom.yu.edu | \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!math.ohio-state.edu!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!gilbertd From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: IUBio archive update Message-ID: Date: 5 Aug 93 17:04:31 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 31 Nntp-Posting-Host: fly.bio.indiana.edu X-Newsreader: TIN [version 1.1 PL8] Here is a list of some of the newer files available at IUBio archive, either thru anonymous ftp or using Internet Gopher to ftp.bio.indiana.edu. ..size...date.....path/name................ 49802 Jun 24 ./biology/teach-soft-chariot.rtf -- biology teaching software catalog 84587 Jun 24 ./biology/teach-soft-intellimation.rtf -- " " 76190 Jun 23 ./molbio/ibmpc/intron-analyzer.uue -- analyze intron data 411550 Jun 20 ./molbio/loopdloop/loopdloop.hqx -- draw & edit rna secondary structure 783939 Aug 1 ./molbio/mac/dnastacks-10m7.hqx -- dna sequence analysis package 146577 Aug 5 ./molbio/mac/embl-email-search.hqx -- EMBL search services by email 303498 Jul 8 ./molbio/mac/macpattern30.hqx -- Protein pattern searches (prosite & blocks) 45877 Jul 21 ./molbio/mac/genedisplay.hqx -- simple sequence editor 56049 Jul 21 ./molbio/mac/molbiolfont.hqx -- font for sequence data 44328 Jul 15 ./molbio/search/mailfasta3.2.shar -- sequence search by e-mail (Unix) 435458 Jun 28 ./molbio/seqapp/seqapp-update.hqx -- update to sequence analysis program 260814 Aug 5 ./util/mac/archivist31.hqx -- your guess is better than mine on this one 29636 Jul 31 ./util/mac/powernotes.hqx -- notebook soft for mac powerbook The gopher service at IUBio has been upgraded to gopher+ over the last few months. There will at some point be newer services available here via gopher+. In some cases there are incompatibilities between gopher- client software and gopher+ servers. I recommend that people upgrade to gopher+ client software. These are available via gopher or ftp to boombox.micro.umn.edu. At some point, I'll add copies of these to IUBio archive also, but the most current gopher+ software is now found at the U. Minnesota boombox site. -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!uts!biobase!pamaga From: pamaga@biobase.aau.dk (Paulo Magalhaes) Newsgroups: bionet.software Subject: PC version of AMPLIFY (or similar) Message-ID: Date: 5 Aug 93 11:50:23 GMT Organization: The Danish BioBase Lines: 36 Hi, I have a known sequence, two primers, and I need to know the following: 1) What PCR products _can_ be made? 2) What are the relative 'probabilities' of each product? (this is, of course, due to things like distance between primers, degree of mispairing, Tm, etc, etc) PLEASE, DON'T TELL ME: a) to change primers b) about a good book on the Principles of PCR c) your own experience in designing perfect primers d) about the weird requests found in bionet.software. I just need a program (for the PC - or even Unix), which can do this. Thank you. All the best from Copenhagen, Paulo -- ********************************************************************** * Paulo Magalhaes | email: pamaga@biobase.aau.dk * * Section of Clinical Genetics | fax: +45 / 31 39 65 43 * * Rigshospitalet | voice: +45 / 35 45 45 92 * * Copenhagen | * * Denmark | snail-mail: C'mon, this is the 90s! * ********************************************************************** -- ********************************************************************** * Paulo Magalhaes | email: pamaga@biobase.aau.dk * * Section of Clinical Genetics | fax: +45 / 31 39 65 43 * * Rigshospitalet | voice: +45 / 35 45 45 92 * From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: bss1jm@surrey.ac.uk (Dr Johnjoe Mcfadden) Newsgroups: bionet.software Subject: gcg package Message-ID: <1993Aug5.111718.19595@gserv1.dl.ac.uk> Date: 5 Aug 93 11:11:11 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 11 Mailer: Elm [revision: 66.25] Original-To: bio-soft@uk.ac.daresbury We are considering buying a Sun Workstation to run molecular biology software packages. Does anybody know how much memory do we need to run the'gcg package' from Genetics Computer Group Inc? Thanks Johnjoe McFadden J.McFadden@uk.ac.surrey From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!BELOIT.EDU!jonesbb From: jonesbb@BELOIT.EDU (Ben Jones) Newsgroups: bionet.software Subject: Re: Looking for MAC pop. biol. software Message-ID: <9308052201.AA10338@beloit.edu> Date: 5 Aug 93 08:13:20 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 53 >I'm looking for a population biology simulation program, similar >to the DOS program POPULUS, which can be run on a very primitive >(floppy drive only) MacIntosh. Any ideas? > >Thanks in advance, >Alex Parker >UMaine Zoology > >aparker@maine.maine.edu I am one of several authors of a Mac application called Biota. It will run on a two-floppy Mac. Biota is part of the BioQUEST Library, which is being marketed by the University of Maryland Academic Software Development Group (ASDG). BioQUEST itself is a non-profit consortium of biologists and programmers at several institutions in the US. Disclaimer: In case I am not biased enough just having helped develop Biota, I also work for BioQUEST. :-) I am not very familiar with Populus, but I will describe the basics of Biota here: Biota allows you to create simulations with up to ten species interacting with each other. Each species can use a different model of growth, and several Models are included from the Population Biology literature. The species are placed in a map which can be divided into up to 144 regions (12 X 12), each of which has a deme of each species. The regions are linked by migration, which can follow one of the built-in migration models or can be completely customized. Simulations to be used for teaching can be saved in a "black box" mode to be used as problems ot be investigated by students. Problem simulations can only be investigated using simulated "field tools". One use of these problem simulations is to create several different models of the same system and try to distinguish them using the field tools. Any technical or scientific comments on Biota should be sent to me. (I am currently working on the next version.) To get sales info, contact ASDG at asdg@umdd.umd.edu. There are both individual licenses (under $100 for the whole library) and site licenses for classroom use. Ben Jones Ben Jones BioQUEST / Department of Biology jonesbb@beloit.edu Beloit College, Beloit, Wisconsin From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!darwin.sura.net!uvaarpa!murdoch!hopper!adamf From: adamf@hopper.ACS.Virginia.EDU (Adam Finkelstein) Newsgroups: bionet.general,bionet.population-bio,bionet.software Subject: RE: Breeding:Performance Evaluation Software Message-ID: Date: 5 Aug 93 12:38:45 GMT Sender: usenet@murdoch.acc.Virginia.EDU Organization: U.Va. Internet Public Access Project Lines: 7 Xref: biosci bionet.general:5665 bionet.population-bio:466 bionet.software:5599 Hello, does anyone have or know of simple spreadsheet software or software templates for performance evaluations to be used in breeding programs? Am using dos/w windows. Thanks, adamf@hopper.acs.virginia.edu From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!math.ohio-state.edu!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: looking for hyperblast Message-ID: Date: 5 Aug 93 19:24:20 GMT References: Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 17 Nntp-Posting-Host: sunflower.bio.indiana.edu The "hyperblast" program that I am familiar with is not publicly available because it uses access to a non-publicly available service from NCBI. The publicly available search service that NCBI provides is their BLAST search by e-mail, and there is a hypercard stack among other programs which you can use to access this: lood at gbsearch-ncbi.hqx at ftp.bio.indiana.edu:/molbio/mac or even at seqapp.hqx at ftp.bio.indiana.edu:/molbio/seqapp I may be wrong about availability of hyperblast and the ncbi immediate blast service that it relies on, but if you don't here anything else publicly here, these are probably not for general use yet/ever. -- Don -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!bcm!raven.imgen.bcm.tmc.edu!bwc From: bwc@bcm.tmc.edu (Robert Cottingham) Newsgroups: bionet.software Subject: Cancer/leukemia DB? Message-ID: <23rk7g$63o@gazette.bcm.tmc.edu> Date: 5 Aug 93 18:40:48 GMT Sender: bwc@raven.imgen.bcm.tmc.edu (Robert Cottingham) Reply-To: bwc@bcm.tmc.edu Organization: Molecular Biology Information Resource, Baylor College of Medicine, Houston, Tx Lines: 19 NNTP-Posting-Host: raven.imgen.bcm.tmc.edu Does anyone know of map databases on cancer or leukemia? We would like to know if such diseases have been mapped by breakpoint or other methods. Or any suggestions on how to find such information would be appreciated. I have tried searching LIMB for the keywords cancer and leukemia but found nothing. I have thought about OMIM/GDB but dont see a straight forward method (without alot of manual effort) for getting a list of OMIM entries with keywords cancer/leukemia and then linking the associated GDB entry to get the map position. Thanks, -Bob ------------------------------------------------------------ Bob Cottingham Phone: 713/798-4275 Cell Biology Fax: 798-5386 Baylor College of Medicine Email: bwc@bcm.tmc.edu Houston, TX 77030 ------------------------------------------------------------ From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!destroyer!cs.ubc.ca!utcsri!newsflash.concordia.ca!mizar.cc.umanitoba.ca!murphy.biochem.umanitoba.ca!user From: dotzlaw@ccu.umanitoba.ca (Helmut Dotzlaw) Newsgroups: bionet.software Subject: Re: looking for hyperblast Message-ID: Date: 5 Aug 93 19:47:54 GMT References: Sender: news@ccu.umanitoba.ca Followup-To: bionet.software Organization: University of Manitoba Lines: 19 Nntp-Posting-Host: murphy.biochem.umanitoba.ca In article , erman@brandeis.edu.bitnet (batu erman) wrote: > I am looking for a program called hyperblast to search genbank from a mac. > Can someone please send me the address that I can ftp it from. > thanks. > Batu Erman Try ftp.bio.indiana.edu, take a look in the molbio/software/mac directory - they have pretty much all of the mol-bio related mac software there. I currently use the NCBI Blast stack, works great! Helmut Dotzlaw University of Manitoba, Faculty of Medicine Department of Biochemistry and Molecular Biology Winnipeg, Manitoba, Canada R3E 0W3 Phone: 204-789-3233 FAX: 204-783-0864 From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!MEDEX.MGH.HARVARD.EDU!RAMAN From: RAMAN@MEDEX.MGH.HARVARD.EDU (Praveena V. Raman) Newsgroups: bionet.software Subject: RNA software Message-ID: <930805142545.108d2@MEDEX.MGH.HARVARD.EDU> Date: 5 Aug 93 18:25:45 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 6 I am posting this question for a colleague of mine - Is there any software that can find an optimal secondary structure for an RNA molecule up to 3000 bases (GCG fold only handles 1200 bases) Any help would be appreciated. Thank you -Praveena raman@medex.mgh.harvard.edu From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!uunet!olivea!charnel!rat!usc!math.ohio-state.edu!uwm.edu!vixen.cso.uiuc.edu!uchinews!kimbark!ecec From: ecec@kimbark.uchicago.edu (Eric Cabot) Newsgroups: bionet.software Subject: Re: Looking for MAC pop. biol. software Message-ID: <1993Aug5.151825.13093@midway.uchicago.edu> Date: 5 Aug 93 15:18:25 GMT References: <93210.154711APARKER@MAINE.MAINE.EDU> Sender: news@uchinews.uchicago.edu (News System) Reply-To: ecec@midway.uchicago.edu Organization: University of Chicago Lines: 22 In article <93210.154711APARKER@MAINE.MAINE.EDU> writes: >I'm looking for a population biology simulation program, similar >to the DOS program POPULUS, which can be run on a very primitive >(floppy drive only) MacIntosh. Any ideas? > >Thanks in advance, >Alex Parker >UMaine Zoology > >aparker@maine.maine.edu You might try to get a hold of PopDyne by Ron J. Etter. I used if for a course I taught once and had the University stock copies for the students to purchase as "textbooks" for about $25/copy. (On the other hand you could get a PC and populus, it is a more comprehensive program than PopDyne.) -- =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=v=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Eric Cabot | "Non Nobis Nati Solum" ecec@midway.uchicago.edu | =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=v=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!math.ohio-state.edu!darwin.sura.net!haven.umd.edu!uunet!munnari.oz.au!bunyip.cc.uq.oz.au!uqvax.cc.uq.oz.au!mail_hoyle From: mail_hoyle@uqvax.cc.uq.oz.au (SIMON HOYLE, ZOOLOGY DEPARTMENT) Newsgroups: bionet.software Subject: Mark-recapture software wanted Message-ID: <1993Aug6.094611.1@uqvax.cc.uq.oz.au> Date: 5 Aug 93 23:46:11 GMT Sender: news@bunyip.cc.uq.oz.au (USENET News System) Organization: University Of Queensland Lines: 21 Nntp-Posting-Host: uqvax.cc.uq.oz.au Hi, an ecological / statistical request. I'm looking for software to analyse capture-recapture data. Something user-friendly, up to date, and capable of open population Jolly-Seber analysis would be nice. The animals in question are wombats, and are/were trapped at the entrances to their burrows. The methodology and the nature of wombats (very sophisticated) means that some of the J-S assumptions are violated, so it would be good to get something more recent than 1990's Fortran JOLLY, which I already have. I'm also writing a model that simulates the movements of wwombats among burrows. Does anyone know of other work along these lines, involving simulation of individuals? Thenks in advance, Simon ___________________________________________________________________________ SIMON HOYLE S.HOYLE@cc.uq.edu.au ZOOLOGY DEPARTMENT The University of Queensland Telephone +61 7 365 2450 Brisbane Qld 4072 AUSTRALIA Facsimile +61 7 365 1655 From owner-software@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!agate!netsys!pagesat!decwrl!tribune.usask.ca!jester.usask.ca!lur From: lur@jester.usask.ca (Rui Lu) Newsgroups: bionet.software Subject: Medline to EndNote?! Message-ID: <23s3j5$6fl@tribune.usask.ca> Date: 5 Aug 93 23:03:01 GMT Sender: Ray Lu Organization: University of Saskatchewan Lines: 12 NNTP-Posting-Host: jester.usask.ca Hi, I remember that there were someone on the net saying, that he can download MedLine files to EndNote? Would 'you' please tell me by E-Mail or post to the net? Thanks. -- Ray Lu | lur@jester.usask.ca or | "When life is a belief, life is a relief." lur@sask.usask.ca | Ph:(306)966-4440/4442 | From owner-software@net.bio.net Thu Aug 05 23:00:00 1993 Path: biosci!POSSUM.MURDOCH.EDU.AU!cummins From: cummins@POSSUM.MURDOCH.EDU.AU (Jim Cummins) Newsgroups: bionet.software Subject: Re: Medline to EndNote?! Message-ID: Date: 6 Aug 93 02:18:38 GMT References: <9308052309.AA08000@net.bio.net> Sender: daemon@net.bio.net Distribution: bionet Lines: 34 Yes, you can use EndNote to download from Medline. In fact you need EndNote Plus with EndLink (interface software). The Medline search needs to be in "Tagged" format and as a text file. I do it routinely, so feel free to email me directly if you have problems. EndNote product info can be got from Avi Rappoport of Niles and Associates on nilesinc@WELL.SF.CA.US To log on to the EndNote Users' newsgroup use the following address: LISTSERV@UCSBVN.BITNET and send the message "SUBSCRIBE ENDNOTE" followed by a carriage return and your name. Dr Jim Cummins +61-9-360 2668 School of Veterinary Studies FAX =61-9-310 4144 Murdoch University cummins@possum.murdoch.edu.au Murdoch, Western Australia 6015 On 5 Aug 1993, Rui Lu wrote: > Hi, > > I remember that there were someone on the net saying, that he can > download MedLine files to EndNote? > > Would 'you' please tell me by E-Mail or post to the net? Thanks. > > -- > Ray Lu | > lur@jester.usask.ca or | "When life is a belief, life is a relief." > lur@sask.usask.ca | > Ph:(306)966-4440/4442 | > From owner-software@net.bio.net Thu Aug 05 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!news.funet.fi!klaava!meikkumac1.pc.helsinki.fi!Heikki.Lehvaslaiho From: Heikki.Lehvaslaiho@Helsinki.FI (Heikki Lehvaslaiho) Newsgroups: bionet.software Subject: Available:"EMBL E-Mail Search" HyperCard stack Message-ID: <23st73$flf@klaava.Helsinki.FI> Date: 6 Aug 93 06:20:19 GMT Organization: University of Helsinki, Finland Lines: 53 NNTP-Posting-Host: meikkumac1.pc.helsinki.fi X-UserAgent: X-XXMessage-ID: X-XXDate: Fri, 6 Aug 93 07:15:38 GMT ---------------------------------------------- "EMBL E-Mail Search" HyperCard stack ---------------------------------------------- "EMBL E-Mail Search" sends formatted e-mail messages to EMBL servers from networked Macs. It requires MacTCP and HyperCard 2.0 or later. The services implemented in "EMBL E-Mail Search" are: - Searching of the current sequence data banks for similarities with a query nucleic acid or protein sequence of yours. Three protocols are available: - Blitz - QUICKSEARCH - FASTA - Retrieval of a sequence in the current molecular data banks by locus name or accession number. "EMBL E-Mail Search" is available by email from netserv@embl-heidelberg.de ("get mac_software:embl-email-search.hqx") or by anonymous ftp from ftp.embl-heidelberg.de as /pub/software/mac/embl-email-search.hqx. Alternatively, you can get it from ftp.bio.indiana.edu as /molbio/mac/embl-email-search.hqx. Both these sites can be accessed by gopher, too. Please send any comments and suggestions you have on this stack to Heikki.Lehvaslaiho@Helsinki.FI I cannot promise any quick answers. If you are having problems with a networking setup at your institution, please check with network experts at your site. EMBL E-Mail Search HyperCard stack is based on "Genbank Search @ NCBI" stack by Don Gilbert. It may be freely used and distributed. The copyright is by Heikki Lehvaslaiho and Don Gilbert. Enjoy, -Heikki Heikki Lehvaslaiho Bitnet:lehvasla@finuh.bitnet X.400: /G=Heikki/S=Lehvaslaiho/O=Helsinki/ADMD=fumail/C=fi/ Meilahti Medical Departments, P.O.BOX 21 (Haartmaninkatu 3) SF-00014 University of Helsinki, FINLAND Phone: +358-0-434 6408 FAX: +358-0-434 6491 From owner-software@net.bio.net Thu Aug 05 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!math.ohio-state.edu!darwin.sura.net!europa.eng.gtefsd.com!eddie.mit.edu!news.mtholyoke.edu!nic.umass.edu!umassd.edu!ulowell!woods.ulowell.edu!chiuf From: chiuf@woods.ulowell.edu Newsgroups: bionet.software Subject: protein structure and hydrophobicity Message-ID: <1993Aug6.134953.1@woods.ulowell.edu> Date: 6 Aug 93 18:49:53 GMT Reply-To: Chiuf@woods.lowell.edu Organization: University of Massachusetts Lowell Lines: 11 NNTP-Posting-Host: aspen.uml.edu I am recently working on a project relating the protein and polymer surface. A software that can analyze the hydrophobicity and/or the surface energy of proteins is in need. Is there anyone knows how and where I could get this? Or is there anyone has the experience working with this? By the way, I will be using the Brookhaven Protein data bank, and I could use either Quntum (or Silicon Graphics) in Unix, or Hyperchem in Windows/IBM in order to run this. Thank you in advance!! Also, I'd like to chat with people who are interested in it. From owner-software@net.bio.net Thu Aug 05 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!math.ohio-state.edu!darwin.sura.net!lhc!ray!dab From: dab@ray.nlm.nih.gov (Dennis Benson) Newsgroups: bionet.software Subject: Re: looking for hyperblast Message-ID: <1993Aug6.203359.20725@nlm.nih.gov> Date: 6 Aug 93 20:33:59 GMT References: Sender: news@nlm.nih.gov Organization: National Library of Medicine Lines: 29 X-Newsreader: Tin 1.1 PL4 gilbertd@sunflower.bio.indiana.edu (Don Gilbert) writes: : The "hyperblast" program that I am familiar with is not publicly : available because it uses access to a non-publicly available : service from NCBI. The publicly available search service that : NCBI provides is their BLAST search by e-mail, and there is : a hypercard stack among other programs which you can use to : access this: lood at gbsearch-ncbi.hqx at ftp.bio.indiana.edu:/molbio/mac : or even at seqapp.hqx at ftp.bio.indiana.edu:/molbio/seqapp : : I may be wrong about availability of hyperblast and the ncbi : immediate blast service that it relies on, but if you don't here : anything else publicly here, these are probably not for general : use yet/ever. : =============== Just to clarify what NCBI is offering publicly --- there is an experimental server/client BLAST service which Don alludes to above. However, this has been considered only a prototype for a server/client application which is under development and which will be made publicly available in the next several months. We'll announce the availability on the bionet.announce newgroup. (Those who have been testing the prototype will continue to be supported, but will be encouraged to switch to the newer version). Dennis Benson NCBI From owner-software@net.bio.net Thu Aug 05 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!math.ohio-state.edu!cs.utexas.edu!uunet!psinntp!execnet!scott.brown From: scott.brown@execnet.com (Scott Brown) Newsgroups: bionet.software Subject: RIP GRAPHICS ANNOUNCEMENT Message-ID: <1.3824.570.0NB085AA@execnet.com> Date: 6 Aug 93 21:17:00 GMT Organization: The Executive Network Information System Lines: 33 NUIQ SOFTWARE INC INTRODUCES RIP MENU DEVELOPMENT TOOL LARCHMONT, NY * July 29, 1993 * NUIQ SOFTWARE INC, a New York based firm specializing in BBS software development announces the release of the RIP Menu Development Tool. The utility, included with the new Powerboard BBS version 1.25A, provides means for BBS operators to design attractive high resolution graphic screens without a drawing program. The elimination of the need for a steady hand, a color monitor, and a mouse will help the operator conver their BBS to one enhanced by mouse control and professional graphics. The menu driven development system facilitates fast and easy integration of RIP graphics into the BBS. The Powerboard software features a script language that allows the building of questionnaires, online games, specialized functions, even re-designing of the entire user interface. The system can be installed in less than 5 minutes after answering 7 simple questions. The initial installation yields a system ready to use with no further configuration. Powerboard BBS software lists for $99 for single-node. Multinode versions start at $175 for a 3-node package. NuIQ Softare, Inc. is constantly striving to remain an innovator of BBS Software technology. An evaluation copy of the software is available. Contact NuIQ by phone, fax, mail, or the product support BBS at 914-834-7830 (hst) 914-833-1479 (v32bis). NuIQ Software, Inc., P.O. Box 832, Larchmont, NY 10538. (914) 833-3479 (914) 833-3623 (fax). From owner-software@net.bio.net Thu Aug 05 23:00:00 1993 Path: biosci!NATURE.BERKELEY.EDU!bosborne From: bosborne@NATURE.BERKELEY.EDU Newsgroups: bionet.software Subject: Re: Medline to EndNote Message-ID: <9308060038.AA14491@nature.berkeley.edu.cnr-net> Date: 6 Aug 93 00:38:57 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 21 >> Hi, >> >> I remember that there were someone on the net saying, that >> he can download MedLine files to EndNote? >> >> Would 'you' please tell me by E-Mail or post to the net? >> Thanks. Yes. One can import references in Medline format directly into an EndNote library using their add-on utility EndLink. I think I bought it from them (Niles and Associates, Berkeley, CA) for about $30. Highly reccomended. I use EndLink v. 1.1.6. Actually, I also have a HyperCard stack that formats references in Agricola format to Medline format, if you ever encounter this problem. ------------------------------------------------------------ Brian Osborne Plant Gene Expression Center bosborne@nature.berkeley.edu Albany CA USA ------------------------------------------------------------ From owner-software@net.bio.net Fri Aug 06 23:00:00 1993 Path: biosci!uwm.edu!linac!uchinews!raistlin!timbuk.cray.com!walter.cray.com!mwd From: mwd@walter.cray.com (Mark Dalton) Newsgroups: bionet.software Subject: Re: RNA software Message-ID: <1993Aug6.193659.20948@walter.cray.com> Date: 7 Aug 93 00:36:58 GMT Lines: 78 Nntp-Posting-Host: calamity.cray.com X-Newsreader: TIN [version 1.2 PL0] FTP sites for RNA folding/viewing software. nrcbsa.bio.nrc.ca: -Michael Zukers software for folding with multiple suboptimal scores, viewing of structures and more. Here is his directory, I have not seen this on the other ftp lists and Michael was all supportive in posting it. (^8 -rw-r--r-- 1 912 900 1084947 Feb 19 11:59 3d_align.tar.Z drwxr-xr-x 2 912 900 4096 Jul 12 19:48 ABJ -rw-r--r-- 1 912 900 1385715 Jun 22 12:51 XRNA.tar.Z -rw-r--r-- 1 912 900 2070835 Oct 13 1992 align.tar.Z -rw-r--r-- 1 912 900 29778 Apr 1 17:18 boxplot.tar.Z -rw-r--r-- 1 912 900 264235 Feb 23 16:06 compbc_dir.tar.Z drwxrwxrwx 2 912 900 512 Apr 27 17:02 donor -rw-r--r-- 1 912 900 856965 Mar 26 1992 ecoli16s.hex.Z -rw-r--r-- 1 912 900 9735 Dec 18 1992 ftp.log -rw-r--r-- 1 912 900 2723437 Jan 19 1993 mfold-2.0.tar.Z -rw-r--r-- 1 912 900 1861467 Jul 29 08:11 mfold-2.2-binaries.tar.Z -rw-r--r-- 1 912 900 887847 Jan 28 1993 mfold-2.2.tar.Z -rw-r--r-- 1 912 900 669424 Jan 4 1993 mfold-cstack.tar.Z -rw-r--r-- 1 912 900 2197599 Jun 4 1992 mfold-dec-2.0.tar.Z -rw-r--r-- 1 912 900 638643 Jun 15 11:32 mfold-dec-2.2.tar.Z -rw-r--r-- 1 912 900 56966 May 26 14:20 mfold-phylo.tar.Z -rw-r--r-- 1 912 900 1398191 May 11 1992 mfold-sun-2.0-nodot.tar.z drwxr-xr-x 7 912 900 512 Jul 16 13:57 mfold-sun-2.2 -rw-r--r-- 1 912 900 465183 Jul 16 13:58 mfold-sun-2.2.tar.Z -rw-r--r-- 1 912 900 862691 Dec 20 1992 mfold-vax-2.0.tar.Z -rw-r--r-- 1 912 900 99815 May 17 15:30 naview.tar.Z -rw-r--r-- 1 912 900 292949 Jul 23 1991 newtree.tar.Z -rw-r--r-- 1 912 900 4005656 Nov 15 1991 phylip.tar.Z -rw-r--r-- 1 912 900 2025073 Oct 30 1991 xmfold-2.0.tar.Z ftp.bio.indiana.edu: Mac RNA structure prediction. Mufold Mac RNA structure display. LoopViewer, LoopDLoop megasun.BCH.UMontreal.CA: GDE (Genetic Data Enviroment) - LoopTool felix.embl-heidelberg.de: Databases: rRNA(ssu), tRNA, smallRNA, berlin life.anu.edu.au: info.mcs.anl.gov: Ribosomal Database Project (Argon Natl. Lab) ncifcrf.gov: RNA information: /pub/shapiro (Bruce Shapiro) /pub/shuyun/newfold /pub/shuyun/sigfold lenti.med.umn.edu: golgi.harvard.edu: GDE's primary home (Steven Smith) ftp.psc.edu: ftp.itc.univie.ac.at: ViennaRNA. The Vienna RNA Package, a new package for folding and comparing RNA secondary structure. RNAfold predict secondary structures RNAeval evaluate energy for given sequence and structure RNAheat calculate melting curves RNAdistance compare secondary structures RNApdist compare ensembles of secondary structures RNAinverse find sequences folding into given structures AnalyseSeqs analyse sequence data AnalyseDists analyse distance matrices -- Mark Dalton Cray Research, Inc. Eagan, MN 55121 Internet: mwd@cray.com From owner-software@net.bio.net Fri Aug 06 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!news.ecn.bgu.edu!wupost!csus.edu!netcom.com!netcomsv!nitelog!dan.jacobson From: dan.jacobson@nitelog.com (Dan Jacobson) Newsgroups: bionet.software Subject: Re: need dna editor for unix Summary: want article reference Keywords: exception Message-ID: <474.321.uupcb@nitelog.com> Date: 4 Aug 93 10:12:00 GMT References: <7408@krafla.rhi.hi.is> Reply-To: dan.jacobson@nitelog.com (Dan Jacobson) Followup-To: comp.os.linux.announce Organization: Nitelog BBS - Monterey, CA - 408-655-1096 Lines: 82 .@FROM :DANJ@WELCHDEV.WELCH.JHU.EDU .@SUBJECT:Re: need dna editor for unix Path: nuchat!menudo.uh.edu!swrinde!elroy.jpl.nasa.gov!usc howland.reston.ans.net!darwin.sura.net!newt.welch.jhu.edu welchdev.welch.jhu.edu!danj From: danj@welchdev.welch.jhu.edu (Dan Jacobson) Message-ID: <1993Aug4.161239.29236@newt.welch.jhu.edu> Sender: news@newt.welch.jhu.edu Nntp-Posting-Host: welchdev.welch.jhu.edu Organization: Johns Hopkins University Genome Data Base (GDB) Date: Wed, 4 Aug 1993 16:12:39 GMT Lines: 68 In article <7408@krafla.rhi.hi.is> php@rhi.hi.is (Petur Henry Petersen) writes: > > Well the title says it all. I need some kind of software that runs >under UNIX which allows me to make comparisons and translate DNA into protein. >Just email me... ThanX > You might want to take a look at GDE (Genetic Data Envronment) - by Steve Smith. You can obtain GDE by gopher or anonymous ftp. Gopher sites: merlot.welch.jhu.edu, select: --> 3. FTP Sites, Software and Data Archives For Biology/ --> 22. GDE (Genetic Data Environment) (Harvard)/ megasun.BCH.UMontreal.CA, select: --> 5. GDE (The Genetic Data Environment)/ Anonymous ftp: golgi.harvard.edu in pub/GDE. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu And from the Readme file I snagged from Tim's site: ----------------------------------------------------------------------------- ...The GDE is a set of programs for multiple sequence alignment and analysis. The GDE currently runs on SUN SparcStations using OpenWindows 2.0 or MIT X11R4. The programs use an expandable user interface which allows the addition of external analysis functions without any rewriting of code. Analysis functions can be written in any language ('C',Fortran, Pascal Basic, shell scripts), and can be seamlessly merged into the systems menu/ dialog box interface. The system supports several data types, nucleic and amino acid sequences, text, and masking sequence, and three forms of color highlighting. The system can handle enormous alignments limited only by the amount of virtual memory on your workstation. Sequences can be edited under several levels of protection, as well as by aligned groups. The system has several external analysis functions included for such things as automated alignment, searching, homology recognition, and phylogenetic analysis. The programs are not in the public domain, but are and will continue to be available for free. Distribution includes full source code, and binaries along with a users manual. Steven Smith ---------------------------------------------------------------------------- . R109U:CLOUD9 From owner-software@net.bio.net Fri Aug 06 23:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software Subject: Re: RIP GRAPHICS ANNOUNCEMENT Message-ID: Date: 7 Aug 93 01:11:22 GMT References: <1.3824.570.0NB085AA@execnet.com> Organization: BIOSCI International Newsgroups for Biology Lines: 9 We don't allow ads on bionet.software. Please don't post one again. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-software@net.bio.net Fri Aug 06 23:00:00 1993 Path: biosci!uwm.edu!wupost!cs.utexas.edu!swrinde!emory!nigel.msen.com!fmsrl7!destroyer!news.itd.umich.edu!nuntius From: johnpher@umich.edu (John Herlocher) Newsgroups: bionet.software Subject: Re: RNA software Message-ID: <240cn1$i7e@terminator.rs.itd.umich.edu> Date: 7 Aug 93 14:03:12 GMT References: <930805142545.108d2@MEDEX.MGH.HARVARD.EDU> Organization: University of Michigan Division of Kinesiology Lines: 4 NNTP-Posting-Host: 35.214.49.10 X-UserAgent: Nuntius v1.1 RNA software Contact DR Zucker for RNA folding software. Their group has developed m-fold2.2, a UNIX based molecular folding progam. Its ported to SGI, SUN, and DEC. Good luck. I hope this is useful. From owner-software@net.bio.net Fri Aug 06 23:00:00 1993 Path: biosci!uwm.edu!wupost!math.ohio-state.edu!sol.ctr.columbia.edu!news.kei.com!eddie.mit.edu!magnesium.club.cc.cmu.edu!news.mic.ucla.edu!library.ucla.edu!psgrain!ee.und.ac.za!hippo.ru.ac.za!cc188.ru.ac.za!g88d4938 From: g88d4938@warthog.ru.ac.za (MR GE DOYLE) Newsgroups: bionet.software Subject: looking - circulatiory sys. sftwre Message-ID: Date: 7 Aug 93 13:06:49 GMT Sender: news@hippo.ru.ac.za (Usenet News Admin) Organization: Rhodes University, Grahamstown, South Africa Lines: 9 Hi Any software out there (preferably ftp-able) about the human (or others) circulatory system? Anything that deals with blook, arteries, heart etc etc? If you can help please let me know, e-mail or newsgroup. Thanx a stack Greg From owner-software@net.bio.net Sat Aug 07 23:00:00 1993 Path: biosci!BSCR.UGA.EDU!arnold From: arnold@BSCR.UGA.EDU Newsgroups: bionet.software Subject: (none) Message-ID: <00970B6F.EB580A40.21453@BSCR.UGA.EDU> Date: 8 Aug 93 16:28:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 175 TO: Those Interested FROM: Jonathan Arnold, ARNOLD@BSCF.UGA.EDU SUBJECT: ODS DISTRIBUTION INFORMATION ON Ordering DNA Sequences (ODS) ver 1.3 (c) 1990 The Univ of GA & A. Jamie Cuticchia PROGRAM DESCRIPTION: Programs are now available to assist in the in vitro reconstruction of chromosomes or chromosome fragments ("contig mapping") from a clonal library. The theory behind the ODS program for "contig mapping" can be found in: Cuticchia, A.J., Arnold, J., and W.E. Timberlake. (1992a). The use of simulated annealing in chromosome reconstruction experiments based on binary scoring. Genetics 132: 591-601 ODS is a program that orders DNA sequences based on similarity of their binary profiles assigned to clones in a library by one of several experimental approaches. The algorithm has been used to map the entire Schizosaccharomyces pombe genome, regions of the Aspergillus nidulans genome, and a region of a human chromosome 9. DNA fragments with a high degree of overlap are expected to show a high degree of similarity in their profiles. The ordering process is based on minimizing the sum of the linking distances between clones as a function of their ordering along the chromosome. The algorithm used to minimize this criterion is a combinatorial optimization method called simulated annealing. The algorithm is described in: Cuticchia, A.J., Arnold, J., and W.E. Timberlake. (1993). ODS: Ordering DNA Sequences, a physical mapping algorithm based on simulated annealing. CABIOS 9, 215-219 Any published use of these programs should cite this reference. Simulated annealing allows approximate heuristic solutions to Np complete problems in a finite amount of time. The annealing parameters in this program are set at the following values: Temperature = 50 Maximum Trials = 500000 Maximum Successes = 25000 Decrease in T = 0.5 PROGRAM INPUT: The program requires answers to three questions. The first is the name of the file which has the binary profile data (INFILE). The second is the name of the file to which the order should be written (OUTFILE). The third is one seed for the random number generator (IDUM). The program will not prompt you for this input, if run interactively, to keep it streamlined for use in a batch queue. PROGRAM OUTPUT: The program outputs the inferred minimum linking distance on the first line, and on succeeding lines, the inferred ordering of clones in the first column and the linking distance between successive clones in the second column. The program also outputs a number of statistics useful in contig identification, such as the probability that a probe hybridizes to a clone and the tail area of an exact test for overlap between two clones. The program presents a reordered data matrix so that a researcher has a graphical display of the map and a sense of how the algorithm ordered the clones in a library. PROGRAM INPUT LIMITATIONS: The length of a binary profile (the number of probes) is limited to 100. The number of clones must be between 1 and 1000. Filenames (with directory path, if specified) must be no longer than 80 characters. The seed can be any integer between -2147483648 and 2147483647. PROGRAM SPEED: The program assembled a complete physical map of 809 clones probed with 92 probes in 3 1/2 minutes on a VAXstation 4000 (12 MIPS). OBTAINING THE SOFTWARE: The software is only distributed via Internet using EMAIL. Please send an EMAIL request to: ARNOLD@BSCF.UGA.EDU ARNOLD@BSCR.UGA.EDU if you wish copies of the program. I will EMAIL you: 1) a FORTRAN program, ODS.FOR; 2) this documentation file, ODS.DOC; 3) a test input file, ODS.DAT; 4) an example output file, ODS.OUT; and 5) a command file, ODS.COM. This last file is what you would use to submit a batch job in the VAX/VMS operating system to generate ODS.OUT. The values were used to generate the output in Cuticchia et al. (1992b). USING THE SOFTWARE WITHOUT THE PROGRAMS: The programs also have been incorporated into a DNA sequence analysis package (Arnold et al., 1986), and can be accessed directly on the Biological Sequence/Structure Computational Facility (BS/SCF). Contact Dr. Weise for a guest account at: WEISE@BSCF.UGA.EDU OBTAINING FURTHER DOCUMENTATION: The best source of documentation are the papers by Cuticchia et al. (1992a, 1992b). A reprint can be obtained by writing: Dr. Jonathan Arnold Genetics Department University of Georgia Athens, GA 30602 or by emailing: ARNOLD@BSCF.UGA.EDU or ARNOLD@BSCR.UGA.EDU SOFTWARE SUPPORT IN THE USE OF THE PROGRAMS: If you have questions about the programs, please contact Dr. A. Jamie Cuticchia currently located at Johns Hopkins University: JAMIE@WELCHGATE.WELCH.JHU.EDU or myself. HARDWARE LIMITATIONS: The programs have been run with minor modification on VAXstations, a DECstation 3100, and on a Silicon Graphics IRIS 4D70/GT workstation. . - - - - - - - - - - - Jonathan Arnold - - - - - - - - - - - - - - - . | Dept. of Genetics, | | University of Georgia | | Athens, Georgia 30602 | | Phone: (706) 542-1449 | | messages: (706) 542-8000 | | FAX: (706) 542-3910 | | Internet: ARNOLD@BSCF.UGA.EDU | | Alternate: ARNOLD@BSCR.UGA.EDU | . - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - . From owner-software@net.bio.net Sun Aug 08 23:00:00 1993 Path: biosci!agate!doc.ic.ac.uk!dapsun.lif.icnet.uk!gea.lif.icnet.uk!not-for-mail From: rmott@gea.lif.icnet.uk (Richard Mott) Newsgroups: bionet.software Subject: software for physical mapping Message-ID: <245ukiINN9dc@gea.lif.icnet.uk> Date: 9 Aug 93 16:39:46 GMT Organization: Imperial Cancer Research Fund Lines: 130 NNTP-Posting-Host: gea.lif.icnet.uk Software Tools for Ordering Clone Libraries from Probe Hybridisation Data ========================================================================= Richard Mott and Andrei Grigoriev Imperial Cancer Research Fund Genome Analysis Laboratory 44 Lincoln's Inn Fields London WC2A 3PX UK email rmott@gea.lif.icnet.uk, a_grigoriev@gea.lif.icnet.uk A suite of programs for manipulating, displaying and ordering probe hybridisation data is now available from the EMBL software server (Netserv@EMBL-Heidelberg.DE - fetch the the file icrf.tar.Z ) and from the authors. The software was written to aid the construction of YAC, P1 and cosmid maps of the fission Yeast S. pombe (Maier et al 1992, Hoheissel et al 1993) and so has been tested thoroughly on real data. Since then the tools described here have been used on a number of other projects both in our own lab and elsewhere. All the programs are written in C, with a subset using the XView and Xlib graphics libraries. The programs are described in Mott et al, 1993. Briefly, in a hybridisation experiment a labelled DNA probe is hybridised onto a filter containing a clone library spotted out in a high-density grid. Clones that are positive for the probe show up as dark spots on an autoradiograph of the filter. If the probe is single-copy then all clones hybridising with it will lie in the same region of the genome, and probes with common positive clones should be neighbours. By hybridising a sufficient number of probes to filters it is possible to order the library into contigs of overlapping clones. The task of ordering libraries is complicated by the fact that experimental noise (miss-scorings, repetitive probes and chimeric clones etc) makes a naive ordering approach untenable, so it was necessary to develop robust ordering algorithms. Those programs that filter or rearrange the data write output files in the same format as the inputs, so that they may be used as inputs to the other applications. For example, the user might extract a subset of the data with one programs, order it with another and then display the results with a third. There are three types of data-file used by the programs; hybridisation data, contig data (lists of contigs, ie ordered probes ) and map data (a list of probes ordered from the genetic map or from some other map). With such a large volume of data an important requirement is to view hybridisation data easily. To this end we have written a PostScript generator, SHOW, which displays a set of probe-clone hybridisations as a matrix, with the probes as columns and the clones as rows. Where a probe and clone hybridise then the corresponding row-column intersection is printed black. If the data have been ordered then contigs appear as overlapping runs of positives. Repetitive probes are immediately apparent as off-diagonal vertical stacks of positives, chimeric clones as off-diagonal horizontal lines and random false positives as isolated dark spots. SHOW can either summarize the entire data-set on a single page, or show it in greater detail spread over several pages. Annotations or labels may be attached to the clones and probes. If the data have been ordered into contigs then the positives should occur in overlapping runs and inconsistencies in the data are then immediately apparent by eye because all the hybridisations to each clone are visible, including those which do not fit well with the current order of clones and probes. This is in contrast with the usual representation of a physical map, where clones are summarised as intervals which have been packed into as few lines as possible. XVSHOW is an XView analogue to SHOW, displaying a scrollable portion of the clone-probe matrix on the screen of a workstation running the OpenWindows window manager. SELECT is a menu-driven program for choosing subsets of hybridisation data. A user can perform Boolean operations to include or exclude clones which hybridise to particular probes or classes of probes. UNHIT is a non-interactive program for selecting clones and probes, which also gives a list of clones not yet hit by a probe. This was used to pick further cosmid probes for {\em S. pombe} when sampling without replacement. FILTER removes clones which are obviously noisy, such as well contaminants, or which hybridise to unrealistically large numbers of probes and thus are very likely to contain highly repetitive elements. REORDER is a tool to reorder a set of clones to a given order of probes. A probe order can be fed into REORDER to generate the clone order, which is then displayed using SHOW. One can optionally specify a set of ``sleeping probes'', which are ignored when ordering the clones but which are output next to the probes used to order the clones. Consequently one may check the consistency of the contigs found with one set of probes (eg cosmid probes on cosmid filters) against the hybridisations of another set (such as YAC probes on cosmid filters). XVEDIT is a contig editor running under Xview which allows the user to edit probe orderings, moving, deleting and inserting probes and contigs and fitting the clones to the resulting orders. It is essentially a graphical interactive version of REORDER. PROBEORDER, BARR and COSTIG are programs for ordering probes. They all assume that the probes are single-copy (although BARR and COSTIG will attempt to filter out probes which are likely to be repetitive), and work by ordering the probes and then fitting the clones to the probe order. PROBEORDER calculates a distance measure between each pair of probes and then uses simulated annealing to find the shortest path connecting all the probes. BARR and COSTIG use heuristic rules to eliminate possible repetitive probes and chimeric clones to clean the data into a consistent set which can then be ordered directly. PATTERNORDER orders clones by computing all pairwise clone distances and then useing simulated annealing to find that order of clones with minimum path length. Hoheisel,J., Maier,E., Mott,R. McCarthy,L., Grogoriev,A., Scwalkwyk,L,,Nizetic,D.,Francis,F., Lehrach,H. (1993) Cell 73:109-120 Maier,E. Hoheissel,J., McCarthy,L., Mott,R., Grigoriev,A., Monaco,A., Larin,Z. and Lehrach,H. (1992) Yeast Artificial chromosome clones spanning the genome of of Schizosaccharomyces pombe. Nature Genetics 1, 273-277 Mott,R. Grigoriev, A. Maier,E. Hoheissel,J., Lehrach, H. (1993) Algorithms and software tools for ordering clone libraries: application to the mapping of the genome of Schizosaccharomyces pombe Nucleic Acids Research 21:1965-1974 From owner-software@net.bio.net Sun Aug 08 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!po.CWRU.Edu!djt2 From: djt2@po.CWRU.Edu (Dennis J. Templeton) Newsgroups: bionet.software Subject: gopher holes for Mol Bio Message-ID: <245tu5$kse@usenet.INS.CWRU.Edu> Date: 9 Aug 93 16:27:49 GMT Reply-To: djt2@po.CWRU.Edu (Dennis J. Templeton) Organization: Case Western Reserve University, Cleveland, OH (USA) Lines: 11 NNTP-Posting-Host: slc12.ins.cwru.edu Our research building has finally been hooked into the internet directly, and I have now the opportunity to poke into some MolBio gopher holes. Several have been posted here and in other forums, but I would appreciate people sending me the addresses of their favorites, which I will collect and repost as a summary. If there is a central catalog of these, it would be nice to post that directly to the group. thanks, dennis From owner-software@net.bio.net Sun Aug 08 23:00:00 1993 Path: biosci!agate!doc.ic.ac.uk!pipex!uunet!newsflash.concordia.ca!sifon!CC.UMontreal.CA!little From: little@ERE.UMontreal.CA (Littlejohn Tim) Newsgroups: bionet.software Subject: Re: gopher holes for Mol Bio Message-ID: Date: 9 Aug 93 22:03:15 GMT References: <245tu5$kse@usenet.INS.CWRU.Edu> Sender: news@cc.umontreal.ca (Administration de Cnews) Organization: Universite de Montreal Lines: 58 >Our research building has finally been hooked into the internet directly, >and I have now the opportunity to poke into some MolBio gopher holes. >Several have been posted here and in other forums, but I would appreciate >people sending me the addresses of their favorites, which I will collect >and repost as a summary. If there is a central catalog of these, it would >be nice to post that directly to the group. There has been some traffic about this on the Bio-Gopher administrators mail list, including a posting of many Bio-Gopher .links. To read the archives of the Bio-Gopher administrators mail list, gopher into and read/ search the postings to this list, point your gopher client at: Name=MegaGopher (Universite de Montreal) Type=1 Port=70 Path= Host=megasun.bch.umontreal.ca --> 3. Bio-Gopher info, links, news, admin...../ --> 3. Biogopher Administrators Information/ --> 2. Mail archive from the BioGopher administrators list/ --> 1. Search Bio-Gopher Admin. postings on MegaGopher +--------------Search Bio-Gopher Admin. postings on MegaGopher---------------+ | | | Words to search for biogopher and list | | | | [Cancel ^G] [Accept - Enter] | | | +----------------------------------------------------------------------------+ 1. little@ERE Re: Bio-Gopher Administrators list. 2. little@ERE Re: Future of the Bio-Gopher Admin List. 3. tim (Tim L Re: Re: Future of the Bio-Gopher Admin List. 4. Jasper Ree Re: Complete BioGopher list? (Was RE: Bio-gopher .links... --> 5. Mike Cherr Re: RE: Complete BioGopher list?. ....... etc.... If anyone is interested in the Bio-Gopher administrators mail list or wants more information on gopher, please just drop me an email. Cheers, Tim ============================================================================== E-mail: little@ere.umontreal.ca Tim Littlejohn tim@bch.umontreal.ca Snail Mail: Departement de biochimie Phone: (514) 343-7936 Universite de Montreal Fax: (514) 343-2210 C.P. 6128, succursale A, Montreal (Quebec), H3C 3J7 CANADA ============================================================================== From owner-software@net.bio.net Sun Aug 08 23:00:00 1993 Path: biosci!agate!doc.ic.ac.uk!pipex!uunet!nih-csl!jowens.nci.nih.gov!jow From: jow@helix.nih.gov (Jim Owens) Newsgroups: bionet.software Subject: Molecular modeling software? Message-ID: <1993Aug9.221532.23004@alw.nih.gov> Date: 9 Aug 93 22:15:32 GMT Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: NIH, Lab of Genetics Lines: 14 X-Xxmessage-Id: X-Xxdate: Mon, 9 Aug 93 18: 15:31 GMT At a party last weekend, I got into a conversation with a Russian emigre, class of '93, who is working at my wife's lab. He was interested in finding out about molecular modeling software. His preference is DOS software, although he will (reluctantly) use Windows or Mac software. I think he also has access to a VAX. I promised to ask on Usenet about such software, since I know nothing about the area. Please e-mail information to me, and if some people ask me to post the results I will gladly post a summary to this newsgroup. Otherwise, I will respond to each individual inquiry. Thanks in advance, Jim Owens From owner-software@net.bio.net Sun Aug 08 23:00:00 1993 Path: biosci!shibumi From: shibumi@net.bio.net (Kenton A. Hoover) Newsgroups: bionet.software Subject: CERT advisory on gophers Message-ID: Date: 9 Aug 93 19:30:34 GMT Reply-To: shibumi@net.bio.net Distribution: bionet Organization: BIOSCI International Newsgroups for Biology Lines: 96 I don't know how many gopher runners haven't heard about or seen this CERT advisory yet, but just in case someone missed it, here it is: Subject: CERT Advisory - UMN UNIX gopher and gopher+ Vulnerabilities Organization: Computer Emergency Response Team : 412-268-7090 =========================================================================== CA-93:11 CERT Advisory August 9, 1993 UMN UNIX gopher and gopher+ Vulnerabilities - --------------------------------------------------------------------------- The CERT Coordination Center has received information concerning vulnerabilities in versions of the UMN UNIX gopher and gopher+ server and client available before August 6, 1993. Vulnerable versions were available on boombox.micro.umn.edu:/pub/gopher/Unix/gopher1.12s.tar.Z, boombox.micro.umn.edu:/pub/gopher/Unix/gopher2.03.tar.Z, and many other anonymous FTP sites mirroring these software versions. We strongly recommend that any site using versions of UMN UNIX gopher and gopher+ dated prior to August 6, 1993 (including version 1.12, 1.12s, 2.0+, 2.03, and all earlier versions) immediately take corrective action. If you have further questions regarding UMN UNIX gopher or gopher+ software, send e-mail to: gopher@boombox.micro.umn.edu - --------------------------------------------------------------------------- I. Description Several vulnerabilities have been identified in UMN UNIX gopher and gopher+ when configured as a server or public access client. Intruders are known to have exploited these vulnerabilities to obtain password files. Other actions may also have been taken by intruders exploiting these vulnerabilities. CERT has already contacted those sites currently known to have been victims of these activities. However, sites may want to check for weak passwords, or consider changing passwords, after installing the new gopher software. II. Impact Anyone (remote or local) can potentially gain unrestricted access to the account running the public access client, thereby permitting them to read any files accessible to this account (possibly including /etc/passwd or other sensitive files). In certain configurations, anyone (remote or local) can potentially gain access to any account, including root, on a host configured as a server running gopherd. III. Solution Affected sites should consider disabling gopherd service and public gopher logins until they have installed the new software. New versions of the UMN UNIX gopher and gopher+ software have been released that provide bug fixes and correct these security problems. Sites can obtain these new versions via anonymous FTP from boombox.micro.umn.edu (134.84.132.2). The files are located in: Filename Size Checksum -------- ------ ----------- Gopher: /pub/gopher/Unix/gopher1.12S.tar.Z 306872 46311 300 Gopher+: /pub/gopher/Unix/gopher2.04.tar.Z 294872 29411 288 - --------------------------------------------------------------------------- The CERT Coordination Center wishes to thank Matt Schroth, Williams College, and others for informing us of these vulnerabilities. We would also like to thank Paul Lindner, University of Minnesota, for his quick response to these problems. - --------------------------------------------------------------------------- If you believe that your system has been compromised, contact the CERT Coordination Center or your representative in FIRST (Forum of Incident Response and Security Teams). Internet E-mail: cert@cert.org Telephone: 412-268-7090 (24-hour hotline) CERT personnel answer 8:30 a.m.-5:00 p.m. EST(GMT-5)/EDT(GMT-4), and are on call for emergencies during other hours. CERT Coordination Center Software Engineering Institute Carnegie Mellon University Pittsburgh, PA 15213-3890 Past advisories, information about FIRST representatives, and other information related to computer security are available for anonymous FTP from cert.org (192.88.209.5). | Kenton A. Hoover | shibumi@net.bio.net | | BIOSCI Network Administrator | | | BIOSCI/IntelliGenetics, Inc. | +1 415 962 7300 | |=============================================================================| From owner-software@net.bio.net Sun Aug 08 23:00:00 1993 Path: biosci!agate!spool.mu.edu!darwin.sura.net!ukma!hsdndev!rascal.med.harvard.edu!kruskal From: kruskal@rascal.med.harvard.edu (Ben Kruskal) Newsgroups: bionet.software Subject: maps of oligos to genes Message-ID: <24642e$s72@hsdndev.harvard.edu> Date: 9 Aug 93 21:02:00 GMT Reply-To: kruskal@rascal.med.harvard.edu Organization: Harvard Medical School / HHMI - Boston, Mass, USA Lines: 17 NNTP-Posting-Host: rascal.med.harvard.edu News-Software: VAX/VMS VNEWS 1.3-4 A request for help! My group studies two genes, and for each we have scores of oligos--perhaps hundreds. We use GCG as our primary manipulation software. I've been looking for a way to map oligos onto the gene sequence to create a nice output (either graphic or sequence based) showing the oligo names positioned along the gene. In GCG, I've tried to use map/mapplot, and the difficulty there is that our oligos often have significant numbers of mismatches (mutations to create restriction sites, or 5' additions to add in other functionalities)--and either map doesn't recognize them, or if the mismatch parameter is tweaked to allow it , then short oligos come up with many false matches. I'm willing to use software other than GCG--we use MicroGenie on a PC, and will soon be acquiring a Mac package (either GeneWorks or MacVector)--or if someone has a standalone package that will run on a PC, Mac or VAX, that would be good too. Thanks for any suggestions. From owner-software@net.bio.net Sun Aug 08 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!gilbertd From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: gopher holes for Mol Bio Message-ID: Date: 9 Aug 93 18:08:22 GMT References: <245tu5$kse@usenet.INS.CWRU.Edu> Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 13 Nntp-Posting-Host: sunflower.bio.indiana.edu X-Newsreader: TIN [version 1.1 PL8] Here is the link for a folder of about 65 bio-gophers, many of which hare molecular in orientation. Type=1+ Name=Other-Bio-Gophers Path=1/Other-Bio-Gophers Host=ftp.bio.indiana.edu Port=70 Admin=Don Gilbert -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-software@net.bio.net Sun Aug 08 23:00:00 1993 Path: biosci!UMBC2.UMBC.EDU!BUSTOS From: BUSTOS@UMBC2.UMBC.EDU Newsgroups: bionet.software Subject: Database of protein binding motifs Message-ID: <01H1JVIJQCZW000FV4@UMBC2.UMBC.EDU> Date: 9 Aug 93 22:54:09 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 15 Dear Bio-soft community: I am interested in gathering information on "confirmed" protein-binding DNA motifs from prokaryotic and eukaryotic origin. Could anyone point me in the direction of a database or some other form of compiled list? As usual, please direct your replies directly to my internet address: bustos@umbc2.umbc.edu I will post a summary of the responses in case someone else is interested in similar information. I thank everyone in advance. Sincerely, Mauricio M. Bustos, Ph.D. Dept. of Biological Sciences University of Maryland Baltimore, MD. From owner-software@net.bio.net Sun Aug 08 23:00:00 1993 Path: biosci!uwm.edu!vixen.cso.uiuc.edu!sdd.hp.com!cs.utexas.edu!wupost!darwin.sura.net!uvaarpa!gmuvax.gmu.edu!ishah From: ishah@gmuvax.gmu.edu Newsgroups: bionet.software Subject: Message-ID: <1993Aug9.111845.54297@gmuvax.gmu.edu> Date: 9 Aug 93 16:18:45 GMT Organization: George Mason University, Fairfax, VA. Lines: 16 I am looking for some C source files (or binaries for a sun4m) to determine a protein sequence for given a nucleotide sequence. References or algorithms would also be welcome. Please send mail to Thanks in advance. Imran Shah C.S.I, George Mason University. From owner-software@net.bio.net Mon Aug 09 23:00:00 1993 Path: biosci!ASPEN.UML.EDU!chiuf From: chiuf@ASPEN.UML.EDU Newsgroups: bionet.software Subject: protein structure and hydrophobicity Message-ID: <9308062030.AA21782@net.bio.net> Date: 6 Aug 93 18:49:53 GMT Sender: daemon@net.bio.net Reply-To: Chiuf@woods.lowell.edu Distribution: bionet Lines: 25 ----------------------------Original message---------------------------- >A software that can analyze the hydrophobicity and/or the surface energy of >proteins is in need. Is there anyone knows how and where I could get this? >Or is there anyone has the experience working with this? >Thank you in advance!! >Also, I'd like to chat with people who are interested in it. ------------------------------------------------------------------------- There is a package available from Hitachi Software (PROSIS), that does some hydrophobicity analysis. It is good, but far from perfect. It runs under DOS. There are more complete software packges for Mac. Sure, I am interested in it ! If you find something really good for Windows or DOS, please let me know. Wagner Fontes Brazilian Center of Protein Sequencing Biochemistry and Protein Chemistry Laboratory University of Brasilia - Brasilia - Brazil From owner-software@net.bio.net Mon Aug 09 23:00:00 1993 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!vincent2.iastate.edu!dangold1 From: dangold1@iastate.edu (Daniel M Goldman) Newsgroups: bionet.software Subject: Advanced Imaging/Image Analysis Message-ID: Date: 10 Aug 93 01:32:55 GMT Sender: news@news.iastate.edu (USENET News System) Organization: Iowa State University, Ames IA Lines: 10 Several people emailed me about Advanced Imaging. This is a trade magazine with articles and advetisements on image analysis and systems. Write for an application for a free subscription: Advanced Imaging 445 Broad Hollow Road Melville NY 11747 You might be able to find a copy to review in a techni technical library. From owner-software@net.bio.net Mon Aug 09 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!darwin.sura.net!spool.mu.edu!agate!doc.ic.ac.uk!warwick!qmw-dcs!qmw!demon!visigoth.demon.co.uk!user From: pettsj@visigoth.demon.co.uk (James Petts) Newsgroups: bionet.software Subject: Sequence Alignmrnt Algorithms Message-ID: Date: 10 Aug 93 00:40:51 GMT Sender: news@demon.co.uk (Usenet Administration) Followup-To: bionet.software Organization: No Affiliation Lines: 14 Nntp-Posting-Host: visigoth.demon.co.uk Hi Can anybody point me in the direction of a comparitive review/description of sequence alignment algorithms? -- ===> James Petts <=== ========================================================================= pettsj@visigoth.demon.co.uk ..oo000oo.. PGP 2.X key on the servers ========================================================================= I feel that if a person can't communicate, the very least he can do is shut up. -- Tom Lehrer ========================================================================= From owner-software@net.bio.net Mon Aug 09 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!darwin.sura.net!newt.welch.jhu.edu!welchdev.welch.jhu.edu!danj From: danj@welchdev.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.software Subject: Re: Molecular modeling software? Message-ID: <1993Aug10.143715.8865@newt.welch.jhu.edu> Date: 10 Aug 93 14:37:15 GMT References: <1993Aug9.221532.23004@alw.nih.gov> Sender: news@newt.welch.jhu.edu Organization: Johns Hopkins University Genome Data Base (GDB) Lines: 38 Nntp-Posting-Host: welchdev.welch.jhu.edu In article <1993Aug9.221532.23004@alw.nih.gov> Jim Owens writes: >At a party last weekend, I got into a conversation with a Russian emigre, >class of '93, who is working at my wife's lab. He was interested in >finding out about molecular modeling software. His preference is DOS >software, although he will (reluctantly) use Windows or Mac software. I >think he also has access to a VAX. I promised to ask on Usenet about >such software, since I know nothing about the area. > Point your gopher client at merlot.welch.jhu.edu and select: --> 3. FTP Sites, Software and Data Archives For Biology/ in this directory you'll find (among other things): --> 2. 3D Protein Display and Sequence Analysis for the PC (UIUC)/ --> 9. CCP4 - Programs for Protein Crystallography (U.K.)/ --> 30. Kinemages, Mage, Pkin -3D Protein Display for the Mac and PC (UIC)/ --> 33. Lots of Molecular Graphics, Dynamics and Chemistry (Brazil)/ --> 38. MULTI, molecular modelling (NIEHS-NIH)/ --> 42. MolViewer - Molecule viewing program for NeXT (Rice)/ --> 53. ProMod - 3D modeling software (Geneva)/ --> 56. RasMol - Molecular Graphics Visualisation tool - Unix and PC (UK)/ --> 57. RasMol - tkrasmol.tar.Z - Extended interface (Berkely) --> 64. XMol - display and analysis of molecular model data (MSC)/ --> 33. Lots of Molecular Graphics, Dynamics and Chemistry (Brazil)/ Numbers 2, 30, and 56 are your best bet for PCs. If someone would like to know more about gopher write me a note and I'll send you some information to help get you started. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-software@net.bio.net Mon Aug 09 23:00:00 1993 Path: biosci!uwm.edu!vixen.cso.uiuc.edu!sdd.hp.com!portal!uunet!digex.com!cdi.digex.net!user From: rosslars@access.digex.net (Bruce Ross-Larson) Newsgroups: bionet.software Subject: HEALTH CENTER Message-ID: Date: 10 Aug 93 19:09:20 GMT Followup-To: bionet.software Organization: Communications Development, Inc. Lines: 19 NNTP-Posting-Host: cdi.digex.net I am trying to establish a resource center in Washindton D.C., the aim of which is to provide a list of health related software and provide displays of some of them. It will be used by health officials from all over the world, especially the developing world, to see how this technology can be used in their health programs. If any companies would be interested in placing a CD-ROM or laserdisc in the resource center please contact me. Many thanks, Christian McCullough. -------------------------------------------------------------- Communications Development, Inc./American Writing Corporation 1075 International Sq. 1825 Eye St. NW Washington, DC 20006 (202) 775-2132 FAX: (202) 775-2135 rosslars@access.digex.net From owner-software@net.bio.net Mon Aug 09 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!swrinde!emory!emoryu1!emoryu1.cc.emory.edu From: bcresas@emoryu1.cc.emory.edu (Scott Sammons) Newsgroups: bionet.software Subject: Re: Sequence Alignmrnt Algorithms Message-ID: <4255@emoryu1.cc.emory.edu> Date: 10 Aug 93 12:48:49 GMT References: Sender: news@emory.edu Reply-To: bcresas@emoryu1.cc.emory.edu Organization: Emory University (BIMCORE) Lines: 11 Nntp-Posting-Host: emoryu1.cc.emory.edu There was one in Computers and Biomedical Research 24, 72-96 (1991). It's a couple of years old, but still mostly relevant. -Scott ============================================================================== | Scott A. Sammons (404) 727-2780 | | Emory University FAX: (404) 727-3659 | | Biomolecular Computing Resource Internet: bcresas@unix.cc.emory.edu | | 3025 Rollins Research Center | | Atlanta, GA 30322 | ============================================================================== From owner-software@net.bio.net Mon Aug 09 23:00:00 1993 Path: biosci!agate!doc.ic.ac.uk!uknet!pipex!uunet!news!demon!visigoth.demon.co.uk!user From: pettsj@visigoth.demon.co.uk (James Petts) Newsgroups: bionet.software Subject: Homology-based model-building query. Message-ID: Date: 10 Aug 93 16:02:14 GMT Sender: news@demon.co.uk (Usenet Administration) Followup-To: bionet.software Organization: No Affiliation Lines: 19 Nntp-Posting-Host: visigoth.demon.co.uk I am looking for opinions as to what is the absolute minimum basic requirement for building a model of a protein based on structural homology with other proteins of known structure. CAn people please e-mail me with their opinions regarding amount of sequence homology, sequence identity, number of homologous proteins, relationship between known structure and sequence etc 3tc. I will summarise and repost. -- ===> James Petts <=== ========================================================================= pettsj@visigoth.demon.co.uk ..oo000oo.. PGP 2.X key on the servers ========================================================================= I feel that if a person can't communicate, the very least he can do is shut up. -- Tom Lehrer ========================================================================= From owner-software@net.bio.net Mon Aug 09 23:00:00 1993 Path: biosci!agate!doc.ic.ac.uk!pipex!uunet!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc.harvard.edu!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.software Subject: Re: Sequence Alignmrnt Algorithms Message-ID: Date: 10 Aug 93 13:11:24 GMT References: Lines: 34 Nntp-Posting-Host: husc10.harvard.edu Tyler, EC, MR Horton, and PR Krause. 1991. Comp.&Biomed Res. 24:72-96. A review of algorithms for molecular sequence comparison. It is a little old now and does not discuss BLAST (a widely-used heuristic algorithm) so you should also check: Altschul, SF, W Gish, W Miller, EW Myers, and DJ Lipman. 1990. JMB 214:1-8. Basic local alignment search tool. FASTDB is another fast heuristic method but I don't have the reference handy (you can find it by gophering to merlot.welch.jhu.edu and looking through SeqAnalRef -- my gopher is down at the moment). A good reference on optimizing the speed of alignment algorithms is: Spouge, JL. 1991. CABIOS 7:1-7. Fast optimal alignment. There are two Methods in Enzymology volumes you should check into also: the Molecular Evolution (183?) volume edited by Russell Doolittle and the Numerical Methods (200-something) volume. The latter contains an excellent description of dynamic programming methods and space-efficient implementations of such. Hope this helps. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@biosun.harvard.edu From owner-software@net.bio.net Tue Aug 10 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!moe.ksu.ksu.edu!hobbes.physics.uiowa.edu!news.uiowa.edu!news.weeg.uiowa.edu!vaxa.weeg.uiowa.edu!AGOODRID From: agoodrid@vaxa.weeg.uiowa.edu Newsgroups: bionet.software Subject: Scan Analysis vs. NIH Image? Message-ID: <1993Aug11.033207.4149@news.weeg.uiowa.edu> Date: 11 Aug 93 03:32:07 GMT Sender: news@news.weeg.uiowa.edu (News) Reply-To: agoodrid@vaxa.weeg.uiowa.edu Organization: U. of Iowa - Weeg Computing Center Lines: 14 Nntp-Posting-Host: vaxa.weeg.uiowa.edu I've come across Scan Analysis (Biosoft) in my new place of work and I'm trying to sort out the usefulness of the program. Has anyone compared these programs for their ability to accurately and easily quantitate signals from Southerns etc.? I not adept at writing macros for NIH Image (just discovered it actually) so I thought I'd put the question to the net. Does anyone know or explain how Scan Analysis calculates the signal it detects? The tech rep at BioSoft was a little vague and the manual we obtained was painfully sparse. Steve LSALATI@WVNVAXA.WVNET.EDU From owner-software@net.bio.net Tue Aug 10 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!dziuxsolim.rutgers.edu!pilot.njin.net!dforan From: dforan@pilot.njin.net (David Foran) Newsgroups: bionet.software Subject: FFT EM Software 3D???? Keywords: FFT EM 3D Message-ID: Date: 11 Aug 93 20:29:27 GMT Organization: Rutgers Univ., New Brunswick, N.J. Lines: 24 Hello, I am working on an SGI computer platform and I am trying to enhance and quantitate EM digital images. 1) Specifically, I am looking for public domain software written in C which allows me to take an FFT, perform spatical filetering, layer line filtration, and perform back projection. 2) In addition, I am interested in locating software which would enable me to determine surface/ envelope points on a molecule reconstructed from a series of contour maps. 3) Does anyone know what the most common or accepted 3-D file format is? Any help would be appreciated........ Thanks in advance, david From owner-software@net.bio.net Tue Aug 10 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!library.ucla.edu!psgrain!ee.und.ac.za!ucthpx!uctvax.uct.ac.za!zubrycki From: zubrycki@uctvax.uct.ac.za Newsgroups: bionet.software Subject: help!!! Looking for prog ARTHUR Message-ID: <1993Aug11.112426.204746@uctvax.uct.ac.za> Date: 11 Aug 93 09:24:26 GMT Organization: University of Cape Town Lines: 6 Hi Does anyone know where to get porgram called ARTHUR. Apparently was available from B.Kowalsi from Univ of Washington, Seatlle Igor Zubrzycki Univ of Cape Town zubrycki@uctvax.uct.ac.za From owner-software@net.bio.net Wed Aug 11 23:00:00 1993 Path: biosci!s.u-tokyo!news.u-tokyo.ac.jp!wnoc-tyo-news!nec-tyo!nec-gw!sgiblab!swrinde!network.ucsd.edu!munnari.oz.au!bruce.cs.monash.edu.au!monu6!vcp1.vcp.monash.edu.au!michael_m From: michael_m@vcp1.vcp.monash.edu.au Newsgroups: bionet.software Subject: Software for CD analysis Message-ID: <1993Aug12.171032.1@vcp1.vcp.monash.edu.au> Date: 12 Aug 93 07:10:32 GMT Sender: news@monu6.cc.monash.edu.au (Usenet system) Lines: 17 Dear Netters I am looking for some software that I can use to deconvolute CD spectra. I have had a go with the program PROSEC (which comes with an AVIV spectropolarimeter) but I was less than impressed with the results. Any suggestions will be welcomed. See you Mike -------------------------------------------------------------------------------- Michael J McLeish Ph.D. | School of Pharmaceutical Chemistry | Phone 61 3 3899540 Victorian College of Pharmacy | FAX 61 3 3899582 381 Royal Parade Parkville 3052 | Email michael_m@vcp.monash.edu.au AUSTRALIA | -------------------------------------------------------------------------------- From owner-software@net.bio.net Wed Aug 11 23:00:00 1993 Path: biosci!daresbury!pg From: pg@mserv1.dl.ac.uk Newsgroups: bionet.software Subject: Gateway changes at Daresbury Message-ID: <24dehm$ps7@mserv1.dl.ac.uk> Date: 12 Aug 93 12:54:14 GMT Reply-To: pg@mserv1.dl.ac.uk Organization: Daresbury Laboratory, UK Lines: 21 NNTP-Posting-Host: dlsj.dl.ac.uk The news-->email gateway service at Daresbury is moving to a new email system to improve reliability and throughput. This should not effect any email users (other than by providing a better service ;->) Any problems should be reported to me at the reply-to address of this message. Yours, Paul P.G.Griffiths. Daresbury Laboratory Graphics/Workstation Development Group - Info-Server Manager JANET/Internet: P.G.Griffiths@dl.ac.uk EARN/BITNET: P.G.Griffiths%dl.ac.uk@UKACRL UUCP: P.G.Griffiths%dl.ac.uk@ukc.uucp From owner-software@net.bio.net Wed Aug 11 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!noc.near.net!saturn.caps.maine.edu!maine.maine.edu!aparker From: APARKER@MAINE.MAINE.EDU Newsgroups: bionet.software Subject: PopDyn address? Message-ID: <93223.202439APARKER@MAINE.MAINE.EDU> Date: 12 Aug 93 00:24:39 GMT Organization: University of Maine System Lines: 5 Sorry to waste bandwidth repeating this. Someone mailed me the address for the author of this program, and I foolishly forgot to log the file. A repeat of the info would be greatly appreciated. aparker@maine.maine.edu From owner-software@net.bio.net Wed Aug 11 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!darwin.sura.net!lhc!azalea!francis From: francis@azalea.nlm.nih.gov (Francis Ouellette) Newsgroups: bionet.software Subject: Re: Where *is* Authorin3.0? Message-ID: <1993Aug12.132056.12427@nlm.nih.gov> Date: 12 Aug 93 13:20:56 GMT References: <24ej5iINNsal@newsman.csu.murdoch.edu.au> Sender: news@nlm.nih.gov Organization: National Library of Medicine Lines: 36 X-Newsreader: Tin 1.1 PL4 torban@csuvax1.csu.murdoch.edu.au (Torban Bennett) writes: : Hi, I have a very quick question. Where is Authorin3.0 available from via : FTP? AuthorIn is now at the NCBI anonymous ftp server (ncbi.nlm.nih.gov) Login as anonymous and use your e-mail address as your password. You will find the Mac version (3.0) in the /pub/authorin/mac directory and the DOS version (1.2) in the /pub/authorin/dos directory. If you have any problems or questions about authorin, its use and availability, please send electronic mail to authorin@ncbi.nlm.nih.gov Other questions about services offered at NCBI can be sent to the address below, regards, francis ========================================================================== NCBI/GenBank Building 38A National Library of Medicine, National Institutes of Health Bethesda, MD, 20894, USA telephone: (301) 496-2475 fax: (301) 480-9241 e-mail: info@ncbi.nlm.nih.gov ========================================================================== From owner-software@net.bio.net Wed Aug 11 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!europa.eng.gtefsd.com!darwin.sura.net!lhc!NewsWatcher!user From: baxevani@ncbi.nlm.nih.gov (Andy) Newsgroups: bionet.software Subject: Re: Software for CD analysis Message-ID: Date: 12 Aug 93 13:34:47 GMT References: <1993Aug12.171032.1@vcp1.vcp.monash.edu.au> Sender: news@nlm.nih.gov Followup-To: bionet.software Organization: NIH Lines: 26 In article <1993Aug12.171032.1@vcp1.vcp.monash.edu.au>, michael_m@vcp1.vcp.monash.edu.au wrote: > > Dear Netters > > I am looking for some software that I can use to deconvolute CD spectra. I > have had a go with the program PROSEC (which comes with an AVIV > spectropolarimeter) but I was less than impressed with the results. Any > suggestions will be welcomed. > Jasco (of J-710 and J-720 fame) have a secondary structure analysis package which is very good -- it will read in spectra data, display it in a number of formats, smooth spectra, calculate % alpha/beta-strand/beta-turn based on Yang and a number of other reference data sets, and does all of the usual mathematical-type stuff. Processed spectra can be dumped to a variety of printers or plotters. It's available without buying a machine (!), but it's pricey -- last time I saw a price list, they listed it for $1000. You might want to find someone who has it and take it for a test-drive before buying. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Andy Baxevanis National Center for Biotechnology Information National Institutes of Health baxevani@ncbi.nlm.nih.gov From owner-software@net.bio.net Wed Aug 11 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!haven.umd.edu!umd5.umd.edu!mbimail.umd.edu!Belas From: Belas@mbimail.umd.edu (Bob Belas) Newsgroups: bionet.software Subject: [Q]IBM program to calc oligo pmol? Message-ID: Date: 12 Aug 93 21:53:25 GMT Organization: Center of Marine Biotechnology Lines: 11 NNTP-Posting-Host: comb15.umd.edu Does anyone know of a shareware or freeware program that calculates the pmolarity of an oligonucleotide give sequence and OD260? Any program that can allow easy calcs of this sort would do. Thanks. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ "Now imagine a Moebius vortex inside a spherical constant, and you've ~~ ~~ got my cosmology." Frank Zappa, 1992. ~~ ~~ ~~ ~~ Bob (Belas@mbimail.umd.edu) ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-software@net.bio.net Wed Aug 11 23:00:00 1993 Path: biosci!rnisd0.DNET.roche.com!delisior From: delisior@rnisd0.DNET.roche.com (Bob DeLisio) Newsgroups: bionet.software Subject: RE: [Q]IBM program to calc oligo pmol? Message-ID: <9308122235.AA07795@mailgate.roche.com> Date: 12 Aug 93 23:07:58 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 32 Bob (Belas@mbimail.umd.edu) writes: > Does anyone know of a shareware or freeware program that calculates >the pmolarity of an oligonucleotide give sequence and OD260? Any program >that can allow easy calcs of this sort would do. Thanks. I simply use the formula: micromolarity = OD260 units x Dilution Factor x 30 micrograms --------------------------------------------- ((A x 312.2) + (G x 328.2) + (C x x288.2) + (T x 303.2) - 61.0) where A=# of A's in an oligo, etc. Of course, micromolarity = picomoles/microliter Hope that helps, Bob ===================================================== _/ _/ Robert DeLisio _/ _/ Roche Institute of Molecular Biology _/ Roche Research Center _/ _/ Nutley, New Jersey 07110-1199 _/ _/ _/ _/ Voice: (201) 235-3728 _/ Fax: (201) 235-2839 _/ _/ Internet: delisior@rnisd0.dnet.roche.com _/ _/ CompuServe: 73517,2616 ===================================================== From owner-software@net.bio.net Wed Aug 11 23:00:00 1993 Path: biosci!T10.LANL.GOV!pgil From: pgil@T10.LANL.GOV (Paul Gilna) Newsgroups: bionet.software Subject: Re: Where *is* Authorin3.0? Message-ID: <9308121409.AA26664@temin.lanl.gov> Date: 12 Aug 93 14:09:32 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 30 Authorin 3.0 (and the earlier 2.1) for the macintosh and Authorin 1.2 for the PC may all be found on the FTP server at LANL. Anonymous FTP to: genome.lanl.gov compressed software and support files are