From owner-software@net.bio.net Tue Feb 01 22:00:00 1994 Path: biosci!bcm!news.msfc.nasa.gov!europa.eng.gtefsd.com!howland.reston.ans.net!agate!msuinfo!harbinger.cc.monash.edu.au!bruce.cs.monash.edu.au!darrenp From: darrenp@bruce.cs.monash.edu.au (Daz) Newsgroups: bionet.software Subject: Re: C++, can we develop collaborative software tools? Date: 2 Feb 1994 01:20:52 GMT Organization: Computer Science, Monash University, Australia Lines: 54 Distribution: bionet Message-ID: <2imv5k$bpl@harbinger.cc.monash.edu.au> References: <2gkb7i$h71@mserv1.dl.ac.uk> NNTP-Posting-Host: dibbler.cs.monash.edu.au X-Newsreader: TIN [version 1.2 251093BETA PL3] Dave Love (d.love@dl.ac.uk) wrote: : >>>>> "Daz" == Daz writes: : Daz> I think C++ is the best : Daz> general purpose programming language around. It's well supported, : Daz> a lot safer than C, more flexible, and allows a high level of : Daz> abstraction, or low level interaction if needed. : I wouldn't argue for a `best' language, but several things in this : thread show up C++ in a bad light against, for instance, Lisp, which : wins as above too: development time; tension between prototyping and : performance; lack of built-in data types; compiler/linker problems; : general clunkiness... I'm not going to get into a language war here - too many of them going on elsewhere anyway, and I won't defend C++ to death either - there are better alternatives for some applications, and I personally find functional programming languages suitable for some kinds of programming - and lisp isn't my first choice in the functional department. Development time is a very hazy term - I can write things very quickly and badly in any langauge - the large number of libraries designed for C++/C makes it very easy to plug in predesigned components. C++ has quite good encapsulation and hiding of implementational detail, so you can go back and get performance later by improving the stuff under the bonnet. Built in types are a two edged sword - they enable slightly better compiler checking and implementation, but are fundamentally inflexible. Anyone who doesn't use the very large number of predefined C++ classes floating around for arrays, strings, hash tables, linked lists etc is missing out on half the things which make C++ nice to use. Does lisp have a built in B-Tree type ? In C++, all I do is include the definitions and use one. 'Compiler/linker problems' is a bit vague. It has a compiler, and it has a linker - and the linker only gives you problems when you have done something naughty (ie it's typesafe which I understand is still not 100% true in lisp programming). The compilers are a little lacking in maturity (in general - borland is very good in this dept.), but the sheer volume of users will fix that quite quickly. C++ is still evolving very rapildy, which is a strong point in my opinion - there haven't been many astounding advances in langauges since the algol generation of compilers, so it's about time people investigated the issues of templated types, object oriented languages etc. C++, whilst not the purest language, is certainly well and truly the fastest, being totally checked at compile time (the latest ansi spec allows run time type checking mind you). General clunkiness: ? details ? Enough said, I shall shut up now. From owner-software@net.bio.net Tue Feb 01 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: paul@enterprise.niehs.nih.gov (Paul Augustine Cardullo) Newsgroups: bionet.software Subject: Re: Using SIMLIFE for intro biology? Date: 2 Feb 1994 00:03:19 -0000 Lines: 22 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2imqk7$olg@mserv1.dl.ac.uk> Original-To: bio-soft@net.bio.net While I have not used SIMLIFE in a classroom setting myself, I have spent quite a bit of time playing with it in my spare time. It is complex enough that it could easily be adapted for use in a classroom setting. The program provides quite a large amount of data on your SimOrganisms. In fact, if you have plenty of disk space, it has a very nice log feature that keeps track of a large number of variables. Though the population size is rather small (the default limit is 200 total animals and a slightly larger number of plants), the program does a rather nice job of presenting the data. In fact, you can even get a look at the gene pool. You can even tinker with the genetic makeup of individuals. (Each animal has about 20 genes that you can control.) All in all, you should be able to whip up a rather nice lesson plan using SimLife. Plus, your students will probably even get a kick out of it. To put in one more gratuitous plug: I hear that another product by Maxis, SimEarth, has also been used in schools, to teach everything from geology to ecology. Oh, the standard disclaimer stuff applies - I have no ties to Maxis, etc. yadda, yadda, yadda Paul A. Cardullo Information Systems and Networks 2327 Englert Dr, Suite 200 RTP, NC 27709 Tel (919)544-6484 e-mail paul@enterprise.niehs.nih.gov From owner-software@net.bio.net Tue Feb 01 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!olivea!news.bu.edu!pfoster From: pfoster@bu.edu (Patricia Foster) Newsgroups: bionet.software Subject: Macaw Date: 2 Feb 1994 03:11:42 GMT Organization: Boston University Lines: 14 Message-ID: <2in5le$hfu@news.bu.edu> NNTP-Posting-Host: acs3.bu.edu X-Newsreader: TIN [version 1.2 PL0] Dear Netters, OK, I *know* this is a Faq, but I did try to search the archives and the connection kept getting aborted. Would some kind person please tell me where to get a manual for Macaw for Windows. Preferably by ftp or gopher. Thanks, pat -- Patricia L. Foster Boston University School of Medicine Boston, MA USA pfoster@bu.edu From owner-software@net.bio.net Tue Feb 01 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!dcl-cs!gdt!aber!localhost!prm From: prm@aber.ac.uk (Pedro Mendes) Subject: Re: Bioinformatics - any definitions welcome? Message-ID: Lines: 23 Sender: news@aber.ac.uk (USENET news service) Nntp-Posting-Host: pcfcdh.dbs.aber.ac.uk Organization: The University of Wales Aberystwyth X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] References: <2imvtd$slb@mserv1.dl.ac.uk> Distribution: bionet Date: Wed, 2 Feb 1994 14:09:05 GMT In article <2imvtd$slb@mserv1.dl.ac.uk> Potter Wickware writes: >I think of it as computer management/analysis of bio-databases. I think >of sequence databases mainly, but I guess the category could also include >such things as trials data, patient info, etc. The crucial element to my >thinking is the presence of a database, and probably quite a large one. This is a very limited view of the subject. There is A LOT of computer applications in biosciences that is completly unrelated with database management and alignment of strings. My work is related with simulations of the dynamics of biochemical systems. I do not deal with databases (not even small), I do not deal with trials data, patient info, etc. nor do I even want to think about sequences (let alone use them). Another thing I know is that what I do is certainly only a small area of what the term BIOINFORMATICS might cover. IMHO, the term is just a trendy word which, if included in a grant proposal, increases the probability of getting funds. Not much use for anything else. Pedro Mendes prm@aber.ac.uk From owner-software@net.bio.net Tue Feb 01 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!psuvax1!psuvm!imeg Organization: Penn State University Date: Wed, 2 Feb 1994 09:07:20 EST From: Sudhir Kumar Message-ID: <94033.090720IMEG@psuvm.psu.edu> Newsgroups: bionet.software Subject: MEGA: Mol. Evol. Gen. Analysis Program Lines: 286 This document contains many pages, including 1. Cover letter 2. Order form (We no longer accept purchase orders) 3. Hardware and software requirements 4. Program upgrade policy 5. Functions in MEGA MEGA version 1.0, 1.01 September, 1993 To whom it may concern: A computer software called MEGA: Molecular Evolutionary Genetics Analysis has been developed. This software is for facilitating statistical studies of molecular evolution by using IBM compatible personal computers. It contains various methods of estimating evolutionary distances and three different methods of phylogenetic inference (UPGMA, neighbor-joining, and maximum parsimony) with either a standard-error test or a bootstrap test of topological differences. For the maximum parsimony method, new algorithms of the branch-and-bound and heuristic searches are implemented. MEGA also computes basic statistical quantities such as nucleotide and amino acid frequencies, transition/transversion bias, codon usage frequencies, number of variable sites, etc. In addition, advance on- screen sequence data and phylogenetic tree editors are included. Integrated and interactive designs, on-line context-sensitive helps, text-file editor, and other unique features make it easy to use MEGA. MEGA version 1.0 is distributed with a nominal fee to defray the cost of producing the user manual (140 pp.) and diskettes, and the mailing and handling expenses (see enclosed order form). However, for anyone who is unable to pay the fee for some reason, it will be provided free of charge after receiving a letter explaining the circumstances. MEGA will not be sent by electronic-mail because the accompanying manual cannot be included in this case. Technical questions and other inquires about MEGA should be directed to the senior author of the software. Please include your electronic-mail address, if any. Sincerely yours, Sudhir Kumar Koichiro Tamura Masatoshi Nei Telephone: (814) 863-7334 FAX: (814) 863-7336 E-mail: imeg@psuvm, imeg@psuvm.psu.edu MEGA ORDER FORM Cost* ----------------------------------------------------------------- Program No Charge User manual, diskette, shipping, and handling $ 15.00 For shipment outside North America add $10.00 _________ (We will use first class airmail) TOTAL _________ ----------------------------------------------------------------- * This cost can be waived if the circumstances for the inability to pay (e.g., lack of hard currencies in some countries) are explained. Diskette type desired: Please specify: [ ] 3.5" Diskette (1.44MB) [ ] DOS Version ...... [ ] 5.25" Diskette (1.2MB) [ ] Computer system... [ ] other (specify).... [ ] Do you use windows? Yes/No All orders must be prepaid in U.S. dollars. Return this form together with a check or money order payable to Penn State University at the following address. Purchase orders will not be accepted. Joyce White Institute of Molecular Evolutionary Genetics The Pennsylvania State University 328 Mueller Laboratory University Park, PA 16802 USA Telephone: (814)-863-7334 Fax: (814)-863-7336 E-mail: IMEG@PSUVM.PSU.edu, IMEG@PSUVM About the user: Name: ____________________________________________ Address: ____________________________________________ ____________________________________________ ____________________________________________ Telephone: _____________________ Fax: _________________ E-Mail: ____________________________________________ --------Hardware and Software------ IBM and IBM-compatible PCs, XTs, ATs, etc. Color/monochrome monitors. 640KB RAM memory. DOS version 3.3 or later. Hard disk with 2MB free. No extended or expanded memory required. No graphics adapters required. No math-chip required. Supports the keyboard as well as the mouse (not essential). ------- Program upgrade policy ---- Since MEGA is in its first version, there may be many software bugs in the program. We are considering to provide registered users a version where bugs reported in version 1.0 and 1.01 will be fixed. As you may notice from the order form, we are just trying to recover the cost of distributing MEGA only. So we are not in a position to provide many upgrades. In any case, we do not plan to include new methods in MEGA soon (for at least one year), and therefore the questions about upgrades may not be so pressing at this moment. -------Functions in MEGA------- Input Input data: DNA sequences RNA sequences Amino acid sequences Distance matrices Input formats: Interleaved sequences Non-interleaved sequences Upper-triangular distance matrix Lower-triangular distance matrix Choice of: Alignment gap symbol Missing-information site symbol Identical site symbol In-memory data editing features Selection: Desired OTUs Domains of sequences Individual sites and codons Codon positions Exclude/include missing information sites Exclude/include alignment gap sites Edit OTU labels Restore OTU labels Sequence data presentation Highlight: Variable sites Parsimony-informative sites Two-fold redundant sites Four-fold redundant sites Translate: Translation of nucleotide sequences into amino acid sequences Output: Formats: MEGA PAUP PHYLIP Publication Data subsets: Only variable sites Only parsimony-informative sites Amino acid sequences translated Codon positions Sequence statistics: Nucleotide and amino acid frequencies Nucleotide pair frequencies in pairwise comparisons Insertion-deletion frequencies Codon usage frequencies Relative synonymous codon usage (RSCU) values Variable sites in overlapping segments Variable sites in nonoverlapping segments Distance estimation Nucleotide substitutions Quantities: Number of nucleotide differences Nucleotide substitutions Transitional substitutions Transversional substitutions Transition/transversion ratio Distance measures: p-distance Jukes-Cantor distance Kimura 2-parameter distance Tajima-Nei distance Tamura distance Tamura-Nei distance Gamma distances Jukes-Cantor model Kimura 2-parameter model Tamura-Nei model Synonymous-nonsynonymous substitutions Genetic code tables: "Universal" Mammalian mitochondrial Drosophila mitochondrial Yeast mitochondrial Computation: Synonymous substitutions Nonsynonymous substitutions Average distances for all pairwise comparisons and standard errors Amino acid substitutions Distance measurers: Number of amino acid differences p-distance Poisson-correction distance Gamma distance Distance output: Control on: Page size Precision for distance output Distance q standard error formats Tree building and test Methods: Neighbor-joining (NJ) UPGMA Maximum parsimony (MP): Branch-and-bound search Heuristic search Statistical Tests: Bootstrap test: Neighbor-joining UPGMA Branch length test: Neighbor-joining Phylogeny editing: Tree re-rooting Swapping and flipping branches Consensus tree Condensed tree Phylogeny printing: Various printers Multiple page printouts Choice of fonts Choice of orientation Choice of page size Tree preview General functions File browsing File editing Exiting to DOS temporarily Context-sensitive Helps Error messages From owner-software@net.bio.net Tue Feb 01 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: "Dr Tristram Wyatt, Continuing Education" Newsgroups: bionet.software Subject: Oxford University Receptors course 14-15 March 1994 Date: 2 Feb 1994 13:00:18 -0000 Lines: 56 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2io852$pec@mserv1.dl.ac.uk> Original-Sender: wyatt@uk.ac.ox.vax Original-To: BIO-SOFTWARE@dl.ac.uk The Oxford Series in Molecular Science Receptors 14 - 15 March 1994 Course Programme Topics covered during the course will include: Day One * Introduction to receptors * Methods * Growth factor receptors * Receptors and oncogenes * G-protein coupled receptors Day Two * Steroid receptors * Insulin receptor * K-channels as drug targets * The industrial approach Course Presenters Dr Steve Ashcroft Dr Antony Galione Dr John Heath Dr Ed Hulme Dr John Knowland Professor Ken Siddle Dr Keith Watling Course Venue: the University's Department for Continuing Education, based in Rewley House, Wellington Square, Oxford. Course Fees Standard course fee: # 440 pounds uk Academics: The full course fee for students is #95 and for other academics #150 which covers tuition, course notes, and daytime refreshments over the two days of the course. Lunch will be an additional #10 per person. A certificate of attendance will be given to participants who attend the whole course. Registration You can reserve a place on the course: By PHONE on: +44 (865) 270285/270286 By FAX on: +44 (865) 270284 Further Information use 'reply' or contact Anna Morris by telephone +44 (865) 270373 or by fax +44 (865) 270284. For queries about administrative matters including registration, fees, accommodation etc. please contact Laura Duffy, CPD Programme Assistant Tel: +44 (865) 270285 Fax: +44 (865) 270284 E-MAIL: CPDMAIL@UK.AC.OXFORD.VAX From owner-software@net.bio.net Tue Feb 01 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Bennett Dyke Newsgroups: bionet.software Subject: Mail problems Date: 2 Feb 1994 05:53:53 -0000 Lines: 53 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2inf5h$9jb@mserv1.dl.ac.uk> Original-To: BioNet Netters: This is a somewhat computer techno-nerdly question, but I need=20 information that I think can only come from from e-mail users,=20 rather than systems people: A significant proportion of our outgoing mail is rejected (timed out)=20 by recipient hosts on an apparently random basis -- for example, I=20 cannot get e-mail through to Oxford University, Penn State, or=20 UCLA. Other destinations, such as Boston U. , Jackson Lab., SUNY=20 Albany, and various university locations in Texas (except Rice=20 University) seem OK. The reason I bring this up on the net is that=20 our problems started after we switched our servers over to Sun's=20 Solaris 2.3. The actual mailer used (Pine, mailx, mush) does not=20 seem to be a factor. We've brought the problem to Sun=D5s attention,=20 and they claim that their software engineers are working on it,=20 although a couple of weeks have passed without a resolution. =20 Apparently we are not the only ones affected, although it's hard=20 to tell -- hence this query. =20 Has anyone been having difficulty in SENDING (as opposed to=20 receiving) mail? Symptoms are Returns with the diagnostic 'Cannot send mail after