From bizzaro at bc.edu Sun Aug 1 18:21:39 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:46 2006 Subject: [Pipet Devel] aglets Message-ID: <37A4C873.3EBBFC35@bc.edu> Greetings. Has anyone heard of IBM's Aglets? This is a system of mobile objects and mobile agents that can traverse the Internet and perform tasks. Here is the link: http://www.trl.ibm.co.jp/aglets It's a slightly different approach from Loci, but again, this might give us some ideas. Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Mon Aug 2 11:29:11 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:46 2006 Subject: [Pipet Devel] ORBit documentation Message-ID: <37A5B947.77644AF9@bc.edu> Locians, I came across some ORBit (C-based CORBA used in Gnome and soon to be used in Loci) documentation. It might be a good place to start for all of us on the list who are new to CORBA: http://www.sanger.ac.uk/Users/birney/orbit-html/book1.htm But what really struck me about this documentation is that it was written by Ewan Birney, a fellow bioinformaticist at the Sanger Center. Perhaps he might like to get involved in Loci. Well, I just sent him a letter. Peter, if you're reading this, maybe Ewan can help interface Loci and EMBOSS :-) It's worth a shot. We need more help with CORBA. Right now Justin (ahem) is working on a Python interface to ORBit. Ta ta, Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Mon Aug 2 14:21:31 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:46 2006 Subject: [Pipet Devel] Thomas Junier joins! References: <37A1CB07.140CBE73@bc.edu> Message-ID: <37A5E1AB.FCB2F5A6@bc.edu> Thomas Junier wrote: > > As a matter of fact, you piqued my curiosity and now I'm itching to learn some > Python. :-) It really is a nice language to work with and has become very popular. The Python home page has a tutorial and other documentation on Python: http://www.python.org/ If you like the old ink-on-paper approach, I highly recommend this book: Mark Lutz and David Ascher Learning Python O'Reilly, 1999 ISBN 1-56592-464-9 You'll also find some links about learning Python with the Gtk+/Gnome GUI widget set at our PyG Tools page: http://bioinformatics.org/pygtools/ If you have any questions about Python, I'd be glad to help...although I'm not an expert. > > Regarding language, as long as a "translator" can connect to CORBA, the > > language shouldn't matter. If we use SEView (or a derivative), we will have to > > work these object models into it. > > I see - although I've no idea of how much work that would imply... We'll find out along the way, but it's our best bet for a universal, language-independent connection between components. So, if someone says, "Eh, I perfer Perl", then they can use Perl. Right now it seems the number of languages used for new development, especially for Linux, is NOT consolidating but rather expanding. Here, for example, are the languages for which Gtk+ bindings exist: Ada95 C++ Dylan Eiffel Guile Haskell JavaScript Objective C Objective Caml Objective Label Pascal Perl Pike Python TOM Pretty impressive. And that doesn't include C, Java, FORTRAN, F, and others that people may want to program in. Can we possibly convince them all to switch to Python? Would it be easier to get them to switch or to get them to use CORBA? > So, I'll gladly join, but I still need some info as to what I should do, and > you folks will have to be patient while I learn all the new things. :-) Great! Well, we're working at a snail's pace here, so don't get impatient; you'll have plenty of time to learn some new things. It may be best to look into CORBA for now, but we don't have a plan laid out yet for implementing it. I just sent this link to the list about some ORBit (C-based CORBA) documentation, if you want to check it out: http://www.sanger.ac.uk/Users/birney/orbit-html/book1.htm > > I can also make an account for you on our server. > > Ok, fine I'll get back to you about that. Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Mon Aug 2 15:04:59 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:46 2006 Subject: [Pipet Devel] message from Gary Message-ID: <37A5EBDB.1A5A32C6@bc.edu> Gary Van Domselaar (who joined Loci) is a teaching assistant at the Canadian Bioinformatics Workshop this week at the University of British Columbia, Vancouver. The Workshop is actually run by Francis Oullette, who is helping with the BioInfo portal here at TOL. I thought you might like to see part of his message to me: The bioinformatics workshop is rocking pretty good right now-- francis oullette is a really cool guy. Most of the other T.A. around here have already heard of the loci project so im pressuring them to join. We'll See! The world is watching, guys! ;-) Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From pmr at sanger.ac.uk Tue Aug 3 05:37:02 1999 From: pmr at sanger.ac.uk (Peter Rice) Date: Fri Feb 10 19:18:46 2006 Subject: [Pipet Devel] ORBit documentation In-Reply-To: <37A5B947.77644AF9@bc.edu> (bizzaro@bc.edu) References: <37A5B947.77644AF9@bc.edu> Message-ID: <199908030937.JAA03140@unst.sanger.ac.uk> Jeff writes: >http://www.sanger.ac.uk/Users/birney/orbit-html/book1.htm > >But what really struck me about this documentation is that it was >written by Ewan Birney, a fellow bioinformaticist at the Sanger >Center. Perhaps he might like to get involved in Loci. Well, I just >sent him a letter. Peter, if you're reading this, maybe Ewan can help >interface Loci and EMBOSS :-) Well, we're certainly thinking about EMBOSS and ORBit. I will be at ISMB 99 in Heidelberg over the coming weekend. I expect a few other Loci list members will be there. Peter -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From tjunier at pcisrec-d402b.unil.ch Tue Aug 3 08:40:04 1999 From: tjunier at pcisrec-d402b.unil.ch (Thomas Junier) Date: Fri Feb 10 19:18:46 2006 Subject: [Pipet Devel] ORBit documentation In-Reply-To: Your message of "Tue, 03 Aug 1999 09:37:02 GMT." <199908030937.JAA03140@unst.sanger.ac.uk> Message-ID: <199908031240.OAA06697@pcisrec-d402b.unil.ch> > I will be at ISMB 99 in Heidelberg over the coming weekend. > I expect a few other Loci list members will be there. I'll be there too, and I look forward to meet other Loci members! Thomas -- Thomas Junier Swiss Institute for Experimental Cancer Research (ISREC) Biocomputing Group - http://pcisrec-d402b.unil.ch/~tjunier From bizzaro at bc.edu Tue Aug 3 14:18:58 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:46 2006 Subject: [Pipet Devel] Loci meeting? (was: ORBit documentation) References: <199908031240.OAA06697@pcisrec-d402b.unil.ch> Message-ID: <37A73292.D18F4491@bc.edu> Thomas Junier wrote: > > > I will be at ISMB 99 in Heidelberg over the coming weekend. > > I expect a few other Loci list members will be there. > > I'll be there too, and I look forward to meet other Loci members! One of these days I'll have the money to travel so far :-) The other meetings coming up are big trips from here (Boston) too: PSB is in Hawaii and RECOMB is in Japan (jeez!). I could have easily made the ISMB 98 in Montreal but ended up missing it :-( But we did have a couple meetings so far where a few Locians actually got to meet each other. I think it would be a great idea to arrange an official Loci meeting that coincides with one of the big bioinformatics conferences. Which one do you guys think would be the best? Where will the following conferences be? ISMB 2000 RECOMB 2001 PSB 2001 Well, we know PSB will be near the Pacific (powerful logical deduction here). Maybe it'll be in California one of these years...but that might be too far for you guys in Europe. BTW, if we manage to get funding for Loci, we may be able to provide travel stipends. But don't hold your breath :-) Ta ta, Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From stein at fmppr.fmnh.org Tue Aug 3 14:22:56 1999 From: stein at fmppr.fmnh.org (J. Steinbachs) Date: Fri Feb 10 19:18:46 2006 Subject: [Pipet Devel] Loci meeting? References: <199908031240.OAA06697@pcisrec-d402b.unil.ch> <37A73292.D18F4491@bc.edu> Message-ID: <37A73380.55485BE0@fmnh.org> > ISMB 2000 > RECOMB 2001 > PSB 2001 > What about the one in Atlanta in November (the second Georgia tech...) ? It's somewhat affordable for those of us who don't have large grants paying for travel... -j -------------------------- Jennifer Steinbachs Computational Biologist Dept. of Botany The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 email: stein@fmnh.org -------------------------- From bizzaro at bc.edu Tue Aug 3 14:35:05 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:46 2006 Subject: [Pipet Devel] Loci meeting? References: <199908031240.OAA06697@pcisrec-d402b.unil.ch> <37A73292.D18F4491@bc.edu> <37A73380.55485BE0@fmnh.org> Message-ID: <37A73659.31C3B8A4@bc.edu> "J. Steinbachs" wrote: > > > ISMB 2000 > > RECOMB 2001 > > PSB 2001 > > > > What about the one in Atlanta in November (the second Georgia tech...) > ? It's somewhat affordable for those of us who don't have large grants > paying for travel... > Hmmm. Do you have a URL for that? The only problem with November is that it's in the middle of the semester :-( Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From stein at fmppr.fmnh.org Tue Aug 3 14:45:29 1999 From: stein at fmppr.fmnh.org (J. Steinbachs) Date: Fri Feb 10 19:18:46 2006 Subject: [Pipet Devel] Loci meeting? References: <199908031240.OAA06697@pcisrec-d402b.unil.ch> <37A73292.D18F4491@bc.edu> <37A73380.55485BE0@fmnh.org> <37A73659.31C3B8A4@bc.edu> Message-ID: <37A738C9.E770E8DA@fmnh.org> "J.W. Bizzaro" wrote: > > "J. Steinbachs" wrote: > > > > > ISMB 2000 > > > RECOMB 2001 > > > PSB 2001 > > > > > > > What about the one in Atlanta in November (the second Georgia tech...) > > ? It's somewhat affordable for those of us who don't have large grants > > paying for travel... > > > > Hmmm. Do you have a URL for that? The only problem with November is that it's > in the middle of the semester :-( > http://exon.biology.gatech.edu/conference/ See the bioinform site for a sizeable list of conferences (http://www.bioinform.com -> calendar) -------------------------- Jennifer Steinbachs Computational Biologist Dept. of Botany The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 email: stein@fmnh.org -------------------------- From bizzaro at bc.edu Tue Aug 3 16:10:13 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:46 2006 Subject: [Pipet Devel] Loci meeting? References: <199908031240.OAA06697@pcisrec-d402b.unil.ch> <37A73292.D18F4491@bc.edu> <37A73380.55485BE0@fmnh.org> <37A73659.31C3B8A4@bc.edu> <37A738C9.E770E8DA@fmnh.org> Message-ID: <37A74CA5.2C90BAF3@bc.edu> "J. Steinbachs" wrote: > See the bioinform site for a sizeable list of conferences > (http://www.bioinform.com -> calendar) Here are some that I picked from the list. Other than the Georgia Tech conference, do any look good? This looks interesting and applicable, but a little too soon for a meeting (much too soon for a poster; maybe next year): * Objects in Bioinformatics focuses upon the role of object-oriented technology, reusable software components, design patterns, and distributed computing in bioinformatics and computational genomics. The conference is aimed at those who are interested in, are developing, or have developed object-oriented software that will be of use to the bioinformatics and genomics community in both academia and industry. Meeting August 23 - 27, 1999, also at the DoubleTree Hotel in San Jose. http://cbcg.lbl.gov/OiB99/ Here are some others: * Bioinformatics: Tools for Genomic Research - September 30-October 1, 1999 - Four Seasons Hotel - Seattle, WA. IBC's 5th Annual International Conference on Bioinformatics is at the forefront of this evolving field, giving delegates an inside view of the hottest trends, newest technologies and applications. http://www.ibcusa.com/2399 * The Institute for Genomic Research (TIGR), Genomic Science Series, THIRD ANNUAL CONFERENCE ON Computational Genomics, November 18-21, 1999, Renaissance Harborplace Hotel in Baltimore, MD http://www.tigr.org/cet/gss/cg/index.html * QUANTITATIVE CHALLENGES IN THE POST-GENOMIC SEQUENCE ERA: A WORKSHOP AND SYMPOSIUM. The La Jolla Interfaces in Science, LJIS, will be hosting a two day workshop on Tuesday, January 11 and Wednesday, January 12 followed by a three day international symposium on Thursday, January 13 - Saturday, January 15, 2000. The workshop and symposium will be held in at the Wyndham Emerald Plaza Hotel in the heart of downtown San Diego's historic Gas Lamp Quarter. http://ljis.ucsd.edu/ljis2000/ A couple more in Europe: * Cambridge Healthtech Institute's Integrative Bioinformatics, January 20-21, 2000 * Zurich, Switzerland. Topics will include: Data Management * Linking Microarrays with Proteomics * Software Tools for Use with Microarrays * Integrating Bioinformatics with Drug Discovery * Progress in Data Visualization * Gene Expression Analysis http://www.healthtech.com/conference/bne2000/bne.htm * ANNOUNCING THE SIXTH GENES, PROTEINS AND COMPUTERS CONFERENCE (GPCVI). GPCVI will be held at Chester College, UK, on WED 26th - FRI 28th April, 2000. The scientific program has yet to be finalised, but will cover the following broad areas: Functional genomics / proteomics, Structural genomics, Sequence analysis / phylogeny, BBSRC Bioinformatics Initiative. http://www.hgmp.mrc.ac.uk/CCP11/gpcvi/gpcvi.html :-) Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From pmr at sanger.ac.uk Tue Aug 3 16:23:13 1999 From: pmr at sanger.ac.uk (Peter Rice) Date: Fri Feb 10 19:18:46 2006 Subject: [Pipet Devel] Loci meeting? In-Reply-To: <37A74CA5.2C90BAF3@bc.edu> (bizzaro@bc.edu) References: <199908031240.OAA06697@pcisrec-d402b.unil.ch> <37A73292.D18F4491@bc.edu> <37A73380.55485BE0@fmnh.org> <37A73659.31C3B8A4@bc.edu> <37A738C9.E770E8DA@fmnh.org> <37A74CA5.2C90BAF3@bc.edu> Message-ID: <199908032023.UAA04113@unst.sanger.ac.uk> >* Objects in Bioinformatics focuses upon the role of object-oriented technology, >reusable software components, design patterns, and distributed computing in >bioinformatics and computational genomics. The first 2 were in Hinxton, organized by Alan Robinson at the EBI, and were excellent. This is the first US OiB meeting. >* ANNOUNCING THE SIXTH GENES, PROTEINS AND COMPUTERS CONFERENCE (GPCVI). GPCVI Great for Europeans (I will be there for sure) but very few Americans seem to turn up to the GPC meetings. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From gvd at redpoll.pharmacy.ualberta.ca Tue Aug 3 16:55:54 1999 From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] Loci meeting? (was: ORBit documentation)\ In-Reply-To: <37A73292.D18F4491@bc.edu> from "J.W. Bizzaro" at Aug 3, 99 06:18:58 pm Message-ID: <199908032055.OAA29414@redpoll.pharmacy.ualberta.ca> > I think it would be a great idea to arrange an official Loci meeting that > coincides with one of the big bioinformatics conferences. Which one do you guys > think would be the best? Where will the following conferences be? > > ISMB 2000 > RECOMB 2001 > PSB 2001 A couple of the bioinformaticians here are at the canadian bioinformatics workshop will be going to the PSB in hawaii -- I think I might try to go too. Jeff, why dont you pressure your prof to send you? Maybe Kenneth can come up with some cash money ;-) BTW I will be in boston from Sept 7 to 21. will you be there too jeff? I was kind of counting on it. --Gary =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca Faculty of Pharmacy Phone: (780) 492-4493 University of Alberta FAX: (780) 492-5305 Edmonton, Alberta, Canada From bizzaro at bc.edu Tue Aug 3 17:23:18 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] Loci meeting? (was: ORBit documentation)\ References: <199908032055.OAA29414@redpoll.pharmacy.ualberta.ca> Message-ID: <37A75DC6.5D0EC996@bc.edu> Gary Van Domselaar wrote: > > A couple of the bioinformaticians here are at the canadian bioinformatics > workshop will be going to the PSB in hawaii -- I think I might try to go > too. Jeff, why dont you pressure your prof to send you? Maybe Kenneth > can come up with some cash money ;-) :-) Heh-heh. Ken may be reading this now. I'm not sure he's so happy with me lately that he'd fork out a couple thousand for me to go to Hawaii. Maybe I'll try to come up with the money myself though. I always wanted to go to Hawaii. Can we get a head-count on everyone who is going to PSB 2000? Is someone sponsoring you, Gary? > BTW I will be in boston from Sept 7 to 21. will you be there too jeff? I > was kind of counting on it. Yep, I'll be here. Send me an e-mail about your plans. I'd like to get together. BTW, I'm planning on giving a talk about Loci at Genome Therapeutics, outside of Boston, on Sept 23. This is part of the Boston Area Molecular Biology Computer Types (BAMBCT) meetings that David Lapointe and I go to. Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From stein at fmppr.fmnh.org Tue Aug 3 17:24:31 1999 From: stein at fmppr.fmnh.org (J. Steinbachs) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] Loci meeting? References: <199908032055.OAA29414@redpoll.pharmacy.ualberta.ca> <37A75DC6.5D0EC996@bc.edu> Message-ID: <37A75E0F.F0BF269@fmnh.org> > Can we get a head-count on everyone who is going to PSB 2000? > I thought about it, but then I wouldn't be able to go to any other conferences next year :( Here's another thought.... What about doing a Loci poster/exhibit/talk at one of the Linux conferences? -j -------------------------- Jennifer Steinbachs Computational Biologist Dept. of Botany The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 email: stein@fmnh.org -------------------------- From bizzaro at bc.edu Tue Aug 3 17:54:43 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] Loci meeting? References: <199908032055.OAA29414@redpoll.pharmacy.ualberta.ca> <37A75DC6.5D0EC996@bc.edu> <37A75E0F.F0BF269@fmnh.org> Message-ID: <37A76523.1D7B37FE@bc.edu> "J. Steinbachs" wrote: > > Here's another thought.... > What about doing a Loci poster/exhibit/talk at one of the Linux > conferences? I've been trying to promote Loci to the open source community as a general-purpose "data-processing system", since the core will not incorporate any biology-specific features. And because nearly all open source applications are for productivity, Loci would fit right in. We could say that Loci is an extension of Gnome, which it really is if we're making use of ORBit, GNORBA, GDOME, GNOME-XML, etc. So yes, we could and probably should present Loci at a Linux or open source conference. My personal desire, however, is to get more involved in bioinformatics than general-purpose programming, so I'd put a bioinformatics conference higher on my priorities list. But that's just me :-) Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From gvd at redpoll.pharmacy.ualberta.ca Tue Aug 3 18:04:07 1999 From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] Loci meeting? In-Reply-To: <37A76523.1D7B37FE@bc.edu> from "J.W. Bizzaro" at Aug 3, 99 09:54:43 pm Message-ID: <199908032204.QAA29644@redpoll.pharmacy.ualberta.ca> > > "J. Steinbachs" wrote: > > > > Here's another thought.... > > What about doing a Loci poster/exhibit/talk at one of the Linux > > conferences? > And Jeff Wrote: > We could say that Loci is an > extension of Gnome, which it really is if we're making use of ORBit, GNORBA, > GDOME, GNOME-XML, etc. So yes, we could and probably should present Loci at a > Linux or open source conference. My personal desire, however, is to get more > involved in bioinformatics than general-purpose programming, so I'd put a > bioinformatics conference higher on my priorities list. But that's just me :-) > I cant see what's stopping us from doing both ;-) --gary =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca Faculty of Pharmacy Phone: (780) 492-4493 University of Alberta FAX: (780) 492-5305 Edmonton, Alberta, Canada From bizzaro at bc.edu Tue Aug 3 18:48:28 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] Loci meeting? References: <199908032204.QAA29644@redpoll.pharmacy.ualberta.ca> Message-ID: <37A771BC.C5889AFD@bc.edu> Gary Van Domselaar wrote: > > I cant see what's stopping us from doing both ;-) Sure, we'll do both. I gathered a number of descriptions below (the O'Reilly one is too soon). But one thing we'll have to consider about these non-scientific conferences, is that they cater to businesses that rent exhibit space. The bioinformatics conferences will have typical, scientific poster-sessions, but I'm not so sure about the Linux conferences; we'll have to look into it further. * FREENIX is a special track within the USENIX Annual Technical Conference. USENIX encourages the exchange of information and technologies between the commercial UNIX products and the free software world as well as among the various free operating system alternatives. FREENIX is the showcase for the latest developments and interesting applications in freely redistributable software. The FREENIX forum includes Apache, FreeBSD, GNOME, GNU, Linux, NetBSD, OpenBSD, Samba, and more. The FREENIX track attempts to cover the full range of software which is freely redistributable in source code form and provides pointers to where the code can be found on the Internet. June 18, 23, 2000, San Diego, CA. http://www.usenix.org/events/usenix2000/cfp/freenix.html * O'Reilly's Open Source Conference. Date: August 21-24, 1999. Location: Monterey Conference Center, Monterey, California, USA. Description: Six parallel Open Source conferences under one roof: The Perl Conference 3.0, plus all-new conferences for Linux, Apache, Tcl/Tk, Python, and sendmail. http://conferences.oreilly.com/ * 3rd Annual Atlanta Linux Showcase. Date: October 12-16, 1999. Location: Cobb Galleria Centre, Atlanta, Georgia, USA. Description: The 3rd annual Atlanta Linux Showcase will feature three conference tracks over three days with 40 speakers discussing the technical and business issues concerning the Linux Operating System. In addition, an exhibition with over 100 vendors, will showcase the latest industry products for Linux. http://www.linuxshowcase.org/ * LinuxWorld Conference & Expo. Date: January 10-13, 2000. Location: Washington DC Convention Center, Washington, DC, USA. Description: This four-day conference is designed to help with developing, integrating, and running a business on the Linux OS. This conference will be a remarkable opportunity for people in a wide variety of job functions to meet and work together to advance the use of Linux. http://www.linuxworldexpo.com/ Buh-bye. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Tue Aug 3 19:33:02 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] Loci meeting? (was: ORBit documentation)\ References: <199908032055.OAA29414@redpoll.pharmacy.ualberta.ca> <37A75DC6.5D0EC996@bc.edu> Message-ID: <37A77C2E.4CBD6355@bc.edu> "J.W. Bizzaro" wrote: > > Gary Van Domselaar wrote: > > > > A couple of the bioinformaticians here are at the canadian bioinformatics > > workshop will be going to the PSB in hawaii -- I think I might try to go > > too. Jeff, why dont you pressure your prof to send you? Maybe Kenneth > > can come up with some cash money ;-) Gary, the next Canadian Bioinformatics Workshop date conflicts with that of PSB 2000. How will they manage that? > Can we get a head-count on everyone who is going to PSB 2000? Has anyone submitted a poster at an earlier PSB? How hard is it to get one "accepted"? How about the others? I heard that ISMB is tough. :-) Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From gvd at redpoll.pharmacy.ualberta.ca Tue Aug 3 20:21:10 1999 From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] Loci meeting? (was: ORBit documentation)\ In-Reply-To: <37A77C2E.4CBD6355@bc.edu> from "J.W. Bizzaro" at Aug 3, 99 11:33:02 pm Message-ID: <199908040021.SAA29765@redpoll.pharmacy.ualberta.ca> Jeff Wrote: > Gary, the next Canadian Bioinformatics Workshop date conflicts with that of PSB > 2000. How will they manage that? The next conference is on genomics, and is a smaller (1 week) course with less instructors and T.As involved (the genomics propellerheads). Im more into proteomics and tool development, as are the others that may be going. You can find out more details about the genomics workshop at http://www.cmmt.ubc.ca/bioinformatics/CourseSummary.html#genomics > > > Can we get a head-count on everyone who is going to PSB 2000? Don't count me in just yet -- I'm gonna have to shmooze pretty hard to get funding for that one, especially cuz bioinformatics is my hobby, not my thesis!! --gary =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca Faculty of Pharmacy Phone: (780) 492-4493 University of Alberta FAX: (780) 492-5305 Edmonton, Alberta, Canada From stein at fmppr.fmnh.org Wed Aug 4 10:51:02 1999 From: stein at fmppr.fmnh.org (J. Steinbachs) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] Loci meeting? References: <199908032204.QAA29644@redpoll.pharmacy.ualberta.ca> <37A771BC.C5889AFD@bc.edu> Message-ID: <37A85356.F8D1426B@fmnh.org> > > I cant see what's stopping us from doing both ;-) > > Sure, we'll do both. I gathered a number of descriptions below (the O'Reilly > one is too soon). But one thing we'll have to consider about these > non-scientific conferences, is that they cater to businesses that rent exhibit > space. The bioinformatics conferences will have typical, scientific > poster-sessions, but I'm not so sure about the Linux conferences; we'll have to > look into it further. > My husband is involved in the Windowmaker project (webmaster/mailing list moderator) and was asked last year to go to some conference to be the Windowmaker presence at their booth/poster/whatever it was (I guess nobody else could go). He couldn't go, but I'll see (1) which Linux thing that was and (2) how they would have gone about it because they too don't have money. -j -------------------------- Jennifer Steinbachs Computational Biologist Dept. of Botany The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 email: stein@fmnh.org -------------------------- From tjunier at pcisrec-d402b.unil.ch Thu Aug 5 05:02:25 1999 From: tjunier at pcisrec-d402b.unil.ch (Thomas Junier) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] Loci meeting? (was: ORBit documentation)\ In-Reply-To: Your message of "Tue, 03 Aug 1999 23:33:02 -0000." <37A77C2E.4CBD6355@bc.edu> Message-ID: <199908050902.LAA10834@pcisrec-d402b.unil.ch> > > Can we get a head-count on everyone who is going to PSB 2000? I'll try to go, if (guess what) I find the cash. > Has anyone submitted a poster at an earlier PSB? How hard is it to get one > "accepted"? How about the others? I heard that ISMB is tough. In my experience, for ISMB it was fairly easy (Well, I submitted just three posters, all in all and counting collaborations, but IMHO there was nothing exceptional on any of them). For talks, on the other hand, that may well be another matter, I've generally been quite impressed by the level of the talks. BTW, will any of you Locians be in Heidelberg this week-end? Thomas -- Thomas Junier Swiss Institute for Experimental Cancer Research (ISREC) Biocomputing Group - http://pcisrec-d402b.unil.ch/~tjunier From bizzaro at bc.edu Sun Aug 8 19:47:24 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] Oh boy, a screenshot! Message-ID: <37AE170C.173909B2@bc.edu> Locians, Here is the latest screenshot of the Loci Workspace. You can see the loci now have multiple inputs (represented by a line with an outlined circle and no arrow) as well as outputs (solid circle with arrow). The number of inputs and outputs (which are highly exaggerated in this screenshot) are predefined, and the lines appear when the locus does. An output can be connected to an input, and visa versa, which will semi-permanently connect two loci. You'll also notice the change in coloring. My thinking is we will have numerous locus (box) shapes (depending on locus function) and one color per shape. The black locus is "selected". I'm also thinking we can have a moderate amount of theme-ing, thanks to Gtk+: The background can be black instead of white, or we could use pixmap tiling. The same applies to other widgets. Cheers. Jeff -------------- next part -------------- A non-text attachment was scrubbed... Name: loci-screenshot-19990808.gif Type: image/gif Size: 16125 bytes Desc: not available Url : http://bioinformatics.org/pipermail/pipet-devel/attachments/19990808/7674a726/loci-screenshot-19990808.gif From bizzaro at bc.edu Wed Aug 11 00:33:47 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] message from James Message-ID: <37B0FD2B.F4DDEF08@bc.edu> Locians, You may know that I've been in contact with James Henstridge over the past year about the Python bindings he has written to GTK+ and GNOME (in case you didn't know, James is one of the primary GNOME developers). Our TOL server also hosts the PyG Tools Information Page. Well, James now has an account on the server, and he and I will be working on some PyGTK documentation. I mentioned to him Loci's need for Python bindings to ORBit, and I thought I'd pass along his reply: As for ORBit bindings, that sounds like a good idea. I don't have much experience with CORBA at the moment, so I don't know how much I would be able to contribute to something like this. I did notice recently that the interface repository daemon for ORBit is starting to become usable. It, together with DII (dynamic invocation interface), should make it possible to do stubless client side bindings, which would simplify things a lot. No shocking revelation, but I hope we can get him to help :-) Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Wed Aug 11 09:36:04 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] CACTVS Message-ID: <37B17C44.55FA730E@bc.edu> Some of you may have heard of CACTVS. It is a chemoinformatics application more than 5 years old, but it's perhaps the closest thing to Loci I have come across. Here is a description of CACTVS. Funny, it could have come right off of the Loci Web page. Jeff --------- CACTVS is a distributed client/server system for the computation, management, analysis and visualisation of chemical information of any, even dynamically and ad-hoc defined type. CACTVS uses a world-wide network of databases with property descriptions, computational modules, data analysis tools, visualization servers, data type handlers and I/O modules to achieve unlimited extensibility of its capacities. The flow of computation is specified by connecting icons representing modules onto workbenches, following the visual programming paradigm. Modules can be obtained from the network of databases, and computations proceed locally or on remote sites, real-time or batch-mode, with controlled access, when these assemblies are flooded with chemical structures representing a dataset. The system consults its network of databases to retrieve information about the necessary steps to obtain some kind of knowledge about a structure. You want to know it - the system will automatically initiate the steps to get it. http://www2.ccc.uni-erlangen.de/software/cactvs/index.html -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Wed Aug 11 10:37:55 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] Re: BNL Open Source References: <93307F07DE63D211B2F30000F808E9E501644D87@edunivexch02.umassmed.edu> Message-ID: <37B18AC3.DCC968AC@bc.edu> "Lapointe, David" wrote: > > I forget. Were you planning on attending this conference? LOCI Poster? I > think I might go to it. > > http://openscience.bnl.gov/ Yeah. Actually, I exchanged some e-mail with the coordinator about TOL and mentioned that I'd like to go. When the announcement was first made, it seemed like a small meeting with only a few speakers and no poster session. I just checked out the Web page again, and now I see it has become a moderately sized conference (for one day). And the fact that they put 1999 in the title indicates this will be an annual meeting. I will be going. And I'm going to consider that poster. I wanted to have a poster for some conference next year, but I don't know how proper it would be to post the same thing at different conferences. But I could always make some changes. Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From gvd at redpoll.pharmacy.ualberta.ca Wed Aug 11 18:50:37 1999 From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] Re: Bioperl: Re: BioML/XML (fwd) In-Reply-To: from "Paul Gordon" at Aug 11, 99 07:42:28 pm Message-ID: <199908112250.QAA15433@redpoll.pharmacy.ualberta.ca> Here is a message recently forwarded to me from my newfound buddy Paul Gordon, who works for the nrc in Halifax, and is the chief programmer (he designed and implemented the interface for MAGPIE: http://www.cbr.nrc.ca/newdocs/services/index.html > MAGPIE This message is from the BioPerl project. > > The XML thread in this group has not been very active recently, but I think > that this community is still interested in the subject, so I am posting this > message here. > > We have recently completed the development of an open and freely-available > source of BIOML (BIOpolymer Markup Language) content, for use by the > bioinformatics community interested in proteins and proteomes. We are > calling it the Proteome Template Library and it is available at > > ftp://204.112.55.140, or at > http://204.112.55.140/PTL. (mime-type=text/xml) > > It consists of approximately 4900 files. Each file represents all of the > protein sequence information, database references and additional information > about a particular species' proteome found in the Protein Identification > Resource (PIR) and NRL3D databases, represented in BIOML. For example, the > BIOML file for Homo sapiens contains all of the protein sequences and > database references for human sequences (~ 15 MB). Any organism with more > than twenty protein sequences in a file has the sequences arranged into a > set of categories, describing either its function, tissue specificity or > subcellular location (if known). > > The library is organised around the NCBI organism taxonomy, so individual > organisms can be found by following the directory structure through to the > appropriate classification. For example, to find "Canis familiaris.bml" > (dog), you look in "Eukaryota", then "Metazoa", then "Chordate", and finally > "Mammalia". If you were not trained in biology, you can search the site > using either a GET or POST request by CGI. For example, to find all proteome > entries matching dog and/or wolf, a request would be made to > http://204.112.55.140/cgi-bin/PtlIndex.exe?words=dog+wolf. The search finds > complete word matches and partial matches and it is case-insensitive. For > example, using just "strep" as the query word will find all of the > Streptococcus and Streptomyces species (as well as several other things). > The reply to the query is in BIOML. > > The complete library is approximately 152 MB. We currently have not packaged > the entire library for download: we will make this available once we are > sure that the library is completely accurate and free of XML bugs. This > release should be considered to be a beta-release: all reports of bugs or > parsing difficulties should be made to bioml@proteometrics.com. These > comments and reports will be posted on a bulletin board, that will be made > available from the main BIOML site (http://204.112.55.140/BIOML). We take > compatibility and parsing difficulties very seriously. > > The BIOML files in the library can be displayed as is, using Internet > Explorer (v. 5). Explorer doesn't deal with large files (> 1 megabyte) very > well, so not all of the files can be viewed in this way. The browser > available at the website can deal with the large files, but it can only be > used on Windows 95, 98 or NT platforms that have IE 4.01 or later installed > on them. > > The standard version of the BIOML DTD has been moved to > http://204.112.55.140/BIOML/bioml.dtd, > because our corporate server was receiving too much BIOML traffic. This new > server is mainly reserved for BIOML. Revised documentation and information > can be obtained at http://204.112.55.140/BIOML. The new and considerably > improved version of the BIOML browser and BIOML Visual Editor for Windows > 95, 98 and NT can be obtained from this site, as well as an open source > version of all of the code used to create the browser. > > Ron Beavis > Proteometrics > > > =========== Bioperl Project Mailing List Message Footer ======= > Project URL: http://bio.perl.org/ > For info about how to (un)subscribe, where messages are archived, etc: > http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html > ==================================================================== > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca Faculty of Pharmacy Phone: (780) 492-4493 University of Alberta FAX: (780) 492-5305 Edmonton, Alberta, Canada From bizzaro at bc.edu Thu Aug 12 08:02:17 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:47 2006 Subject: [Pipet Devel] Loci meetings and presentations Message-ID: <37B2B7C9.566D465@bc.edu> My fellow Locians, I may have mentioned some of this before, but I will list here all the upcoming events for Loci. ----------- LOCI '99 When? September 7-21, 1999 (one day; exact date and time to be determined) Where? Somewhere in the Boston area (place to be determined) This is to be the first official meeting of people involved in Loci and The Open Lab. Discussion topics include Loci design, publication, and funding. It was initiated because Gary will be in Boston for those two weeks. Also likely to attend (besides me) are Ken Marx, David Lapointe, and maybe Robert Harrison. I don't expect anyone to come from a long distance; those I listed are in the U.S. northeast. ----------- BAMBCT SHOW-AND-TELL When? Thursday, September 23, 1999, at 4PM Where? Genome Therapeutics Corp, Waltham, Massachusetts Yours truly will give a 15 minute presentation on Loci in a special "show-and-tell" meeting of the Boston Area Molecular Biology Computer Types (BAMBCT). David Lapointe should be there too. ------------ OPEN SOURCE / OPEN SCIENCE '99 When? Saturday, October 2, 1999, all day Where? Brookhaven National Laboratory, Upton (Long Island), New York I will have a poster and maybe a running demo of the Workspace at the conference. It really seems like it'll be a nice conference to attend. I may carpool with David and someone else. If you want more info on this, check out the Web site: http://openscience.bnl.gov/ ------------- PACIFIC SYMPOSIUM ON BIOCOMPUTING 2000 ???? LOCI 2000 ???? When? January 4-9, 2000 Where? Honolulu, Hawaii Some big question marks on this one. I may make this a vacation with my two brothers, which will mean it'll cost less for me :-) I would submit a poster on Loci. If I do what it takes to pull off a trip like this, I'd definitely want to have a Loci meeting at the same time. So far, I think Gary will go, and Jennifer and Thomas Junier might be able to go. But we still haven't heard from the vast majority here. LET ME KNOW, PLEASE. http://www.cgl.ucsf.edu/psb/ -------------- Well, it looks like I'll be busy very shortly! Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From stein at fmppr.fmnh.org Thu Aug 12 12:44:29 1999 From: stein at fmppr.fmnh.org (JES) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] Loci meetings and presentations References: <37B2B7C9.566D465@bc.edu> Message-ID: <37B2F9ED.481F9176@fmnh.org> > PACIFIC SYMPOSIUM ON BIOCOMPUTING 2000 ???? LOCI 2000 ???? > > When? January 4-9, 2000 > Where? Honolulu, Hawaii > > Some big question marks on this one. I may make this a vacation with my two > brothers, which will mean it'll cost less for me :-) I would submit a poster on > Loci. If I do what it takes to pull off a trip like this, I'd definitely want > to have a Loci meeting at the same time. So far, I think Gary will go, and > Jennifer and Thomas Junier might be able to go. But we still haven't heard from > the vast majority here. LET ME KNOW, PLEASE. > > http://www.cgl.ucsf.edu/psb/ > Heh... I've managed to convince my hubby that a week in Hawaii would be fun, especially so close to my barf-day - er, birthday. So I guess I'll be going and dragging him along - he'll be interested in the "computing" part, not the "bio" part ;-) This means that we won't be going to the Atlanta Linux Expo :( But then... Atlanta... Hawaii... Atlanta.... Hawaii.... Seems like a no-brainer to me. -j -------------------------- Jennifer Steinbachs, PhD Computational Biologist Dept. of Botany The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 email: stein@fmnh.org -------------------------- From bizzaro at bc.edu Thu Aug 12 13:13:27 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] Loci meetings and presentations References: <37B2B7C9.566D465@bc.edu> <37B2F9ED.481F9176@fmnh.org> Message-ID: <37B300B7.DBD7DFE5@bc.edu> JES wrote: > > Heh... I've managed to convince my hubby that a week in Hawaii would be > fun, especially so close to my barf-day - er, birthday. So I guess I'll > be going and dragging him along - he'll be interested in the "computing" > part, not the "bio" part ;-) This means that we won't be going to the > Atlanta Linux Expo :( But then... Atlanta... Hawaii... Atlanta.... > Hawaii.... Seems like a no-brainer to me. So, let's start a list here. GOING TO PSB 2000 YES MAYBE NO NO REPLY ---------------------------------------------------------------------- Bizzaro Junier Williams Van Domselaar Cohen Steinbachs Rice Lapointe Villa Beck Mangalam Zuazaga Bradford Harrison St. Onge Marx Hinsen Jain de Lahondes Sicheritz Triche A couple I didn't list here probably won't be interested in a biological conference. The rest, almost a dozen more, are lurkers on the list, from whom I'd like to hear too. Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From justin at ukans.edu Thu Aug 12 17:07:12 1999 From: justin at ukans.edu (Justin Bradford) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] Loci meetings and presentations In-Reply-To: <37B2B7C9.566D465@bc.edu> Message-ID: > LOCI '99 > > When? September 7-21, 1999 (one day; exact date and time to be determined) > Where? Somewhere in the Boston area (place to be determined) If we can do this on a weekend (or near a weekend), I might be able to fly up. Also, just to let everyone know, I'm going to be offline for several days (driving halfway across the country starting tomorrow). Justin From bizzaro at bc.edu Mon Aug 16 10:51:35 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] [Fwd: Meta-Application again...] Message-ID: <37B82577.82A006A4@bc.edu> Ferdinando, I guess someone just replied to your old post on the Gnome list. Jeff -------------- next part -------------- An embedded message was scrubbed... From: Svanberg Liss Subject: Meta-Application again... Date: Mon, 16 Aug 1999 16:24:38 +0200 Size: 3425 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990816/70d16375/attachment.mht From bizzaro at bc.edu Mon Aug 16 15:33:09 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] Re: SV: Meta-Application again... References: <40DEF2EE1151D311BC520050047B41450186BD@195-66-34-2.itv.se> Message-ID: <37B86775.CC5D27EC@bc.edu> Svanberg Liss wrote: > > Ahh, this was exactly what I was looking for... :) I was just going to ask you to join the list, but I notice you already have :-) > ( The only drawback is that I have to learn Phyton... ;) Not exactly. We're trying to make Loci language-independent. The Workbench/Workspace is written in Python and will serve as one of the main components, but everything will be modular, with CORBA serving as the basic glue. So, providing language X has CORBA bindings, you should be able to use it to make new modules (loci). Most of the Loci developers in fact prefer C, and there are some Perl and Java gurus here too. Are you a programmer or just looking for a new app to use? From your message, it seems you know a bit about some of the Gnome paradigms like Bonobo. We are in great need of some help with this stuff. If you can help, it would be greatly appreciated! I can give you an account on our server with CVS access. Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From Alan at MolBio.org Mon Aug 16 20:01:48 1999 From: Alan at MolBio.org (Alan J. Williams) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] Loci meetings and presentations In-Reply-To: <37B300B7.DBD7DFE5@bc.edu> Message-ID: On Thu, 12 Aug 1999, J.W. Bizzaro wrote: > So, let's start a list here. > > GOING TO PSB 2000 > > YES MAYBE NO NO REPLY > ---------------------------------------------------------------------- Williams I'd love to go, but my wife is due (baby) on Jan 1st. Don't think she'd appreciate me running off to a bioinformatics conference :) -------------------------------------------------------------------- Alan Williams Where observation is concerned, Alan@MolBio.org chance favors the prepared mind. http://www.MolBio.org/cv/ -- Louis Pasteur -------------------------------------------------------------------- ** University of California, Botany Department, Riverside ** From stein at fmppr.fmnh.org Mon Aug 16 22:08:49 1999 From: stein at fmppr.fmnh.org (J. Steinbachs) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] Loci meetings and presentations In-Reply-To: Message-ID: On Mon, 16 Aug 1999, Alan J. Williams wrote: > > I'd love to go, but my wife is due (baby) on Jan 1st. Don't think she'd > appreciate me running off to a bioinformatics conference :) > Heh... Bring the whole family ;-) Kids under 2 travel free :) And I think that moms with kids under 2 days should definitely travel free. United Airlines might disagree though. -j -------------------------------------- Jennifer Steinbachs Computational Biologist Department of Botany Field Museum of Natural History Chicago, IL 60605-2496 e-mail: stein@fmnh.org URL: http://www.plantsex.org -------------------------------------- "I know nothing about Macs." From stein at fmppr.fmnh.org Tue Aug 17 15:37:36 1999 From: stein at fmppr.fmnh.org (JES) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] software find References: Message-ID: <37B9BA00.76F2B404@fmnh.org> Greetings all... I have this recently-acquired spiffy Intel box (running Linux of course) and I need something to run on it... I've been downloading and trying to compile stuff to give this machine a little workout. I discovered something nifty :) I thought I had seen reference to this package somewhere on this list, but I can't seem to find it in my collection of messages (apologies if this is a double posting). http://www.mikro.biologie.tu-muenchen.de/ http://www.mikro.biologie.tu-muenchen.de/pub/ARB/ A little bit more tweaking and I might have it functional. Cheers, -j -------------------------- Jennifer Steinbachs, PhD Computational Biologist Dept. of Botany The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 email: stein@fmnh.org -------------------------- From David.Lapointe at umassmed.edu Wed Aug 18 14:25:15 1999 From: David.Lapointe at umassmed.edu (Lapointe, David) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] FW: Announce: ProtSuite - first developers beta release version Message-ID: <93307F07DE63D211B2F30000F808E9E501644DAE@edunivexch02.umassmed.edu> This just in... -----Original Message----- From: adam moore [mailto:paxamr@unix.ccc.nottingham.ac.uk] Sent: Wednesday, August 18, 1999 9:33 AM To: Perl-XML Mailing List Subject: Announce: ProtSuite - first developers beta release version The BioDOM project announces its first major software release: ProtSuite - A client-side customisable hypermedia system for linking into biomolecular databases. A collection of perl and perl/Tk scripts that use XML and DOM processing to convert text queries over biomolecular databases into a local XML repository of sequences and structures of interest to YOU. This is mainly a developers release, although all are free to download it, the program still has many rough edges, and should not be considered stable for long term use at this stage. The program is available under the GPL/Artistic license for FREE and is available from: http://ala.vsms.nottingham.ac.uk/biodom/software/ The release includes all necessary associated perl modules and ancilliary programs. The program is currently UNIX only and has so far only been tested under Linux (SuSE 6.1). Please download it, have a look and then LET ME KNOW what you think - I would really appreciate all feedback. Known issues/bugs: The PDB parser is alpha and currently in revision The SwissProt parser has not fully been tested against the new release (38) There is no error reporting/debugging info. Adam Moore Virtual School of Molecular Sciences School of Pharmaceutical Science, University of Nottingham http://www.vsms.nottingham.ac.uk/vsms/ Personal Page:http://www.ccc.nottingham.ac.uk/~paxamr/ --- You are currently subscribed to perl-xml as: [david.lapointe@umassmed.edu] To unsubscribe, forward this message to leave-perl-xml-65677R@lyris.activestate.com For non-automated Mailing List support, send email to ListHelp@ActiveState.com From stein at fmppr.fmnh.org Thu Aug 19 17:57:06 1999 From: stein at fmppr.fmnh.org (JES) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] Loci meetings and presentations References: <37B2B7C9.566D465@bc.edu> Message-ID: <37BC7DB2.6BD9C7F8@fmnh.org> For those who are planning to go to PSB 2000... A cautionary note... the group hotel rates don't actually take effect until JANUARY 3. Cheers, -j -------------------------- Jennifer Steinbachs, PhD Computational Biologist Dept. of Botany The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 email: stein@fmnh.org -------------------------- From bizzaro at bc.edu Thu Aug 19 22:53:20 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] Loci meetings and presentations References: <37B2B7C9.566D465@bc.edu> <37BC7DB2.6BD9C7F8@fmnh.org> Message-ID: <37BCC320.526FA5D2@bc.edu> JES wrote: > > For those who are planning to go to PSB 2000... > > A cautionary note... the group hotel rates don't actually take effect > until JANUARY 3. Do you mean the rates posted on the PSB homepage? Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From stein at fmppr.fmnh.org Thu Aug 19 23:47:17 1999 From: stein at fmppr.fmnh.org (J. Steinbachs) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] Loci meetings and presentations In-Reply-To: <37BCC320.526FA5D2@bc.edu> Message-ID: On Fri, 20 Aug 1999, J.W. Bizzaro wrote: > JES wrote: > > > > For those who are planning to go to PSB 2000... > > > > A cautionary note... the group hotel rates don't actually take effect > > until JANUARY 3. > > Do you mean the rates posted on the PSB homepage? > > Correct. So, if you want to spend a full week, say arriving Sunday, then you can arrange to check in and pay piles of cash for Sunday night, stay in the same room and still get the group/meeting rate for the rest of the nights during the meeting. "Piles of cash" = $340/night for the least expensive room (city view?) and $400/night for mountain view. According to meeting organizers, more rooms might be available at group rates (before the meeting begins) about 2 months prior to the meeting, depending on room availability. Airfare from Chicago is going for about $975 (nonstop) right now - that includes the meeting discount on United Airlines. -j -------------------------------------- Jennifer Steinbachs Computational Biologist Department of Botany Field Museum of Natural History Chicago, IL 60605-2496 e-mail: stein@fmnh.org URL: http://www.plantsex.org -------------------------------------- "I know nothing about Macs." From bizzaro at bc.edu Fri Aug 20 10:14:23 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] Loci meetings and presentations References: Message-ID: <37BD62BF.D98157FB@bc.edu> "J. Steinbachs" wrote: > > Correct. So, if you want to spend a full week, say arriving Sunday, then > you can arrange to check in and pay piles of cash for Sunday night, stay > in the same room and still get the group/meeting rate for the rest of the > nights during the meeting. "Piles of cash" = $340/night for the least > expensive room (city view?) and $400/night for mountain view. According > to meeting organizers, more rooms might be available at group rates > (before the meeting begins) about 2 months prior to the meeting, depending > on room availability. Ah. Are there any less expensive hotels in the area? I think Waikiki beach is cluttered with hotels. > Airfare from Chicago is going for about $975 (nonstop) right now - that > includes the meeting discount on United Airlines. When I checked, a couple weeks ago, airfare from Boston (one stop - in Chicago :-) was $1,015 ($40 to Chicago aint bad, huh?). That was also United. Prices will keep going up though. :-) Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From stein at fmppr.fmnh.org Fri Aug 20 12:51:11 1999 From: stein at fmppr.fmnh.org (JES) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] Loci meetings and presentations References: <37BD62BF.D98157FB@bc.edu> Message-ID: <37BD877F.CB575C0C@fmnh.org> "J.W. Bizzaro" wrote: > Ah. Are there any less expensive hotels in the area? I think Waikiki beach is > cluttered with hotels. > > > Airfare from Chicago is going for about $975 (nonstop) right now - that > > includes the meeting discount on United Airlines. > > When I checked, a couple weeks ago, airfare from Boston (one stop - in Chicago > :-) was $1,015 ($40 to Chicago aint bad, huh?). That was also United. Prices > will keep going up though. If only it had been $40 when I drove from CT to look for an apt a few months ago. Looking at the current prices for the Sheraton Waikiki rooms on their web page (link from the meeting web page), the meeting group rates for rooms are a real bargain - especially given the time of year. But if you want to poke around and explore cheaper options, I found a useful link with lots of hotel info and pricing: http://Hawaii-hotels.com/index.html Mapquest doesn't have routing information, but http://www.mapblast.com does just in case you want to check distances (so you're not hiking miles everyday between your alternate hotel and the sheraton). BTW, we will be going out on the 2nd, returning to Chicago on the 9th - luckily, I over-budgeted for hotel expenses (but nobody back home will be getting tacky tourist trinkets!). It might be nice to get a few people together to rent a van or something for a day either before the conference or *gasp* during the conference. Cheers, -j -------------------------- Jennifer Steinbachs, PhD Computational Biologist Dept. of Botany The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 email: stein@fmnh.org -------------------------- From bizzaro at bc.edu Mon Aug 23 14:04:34 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] study time! Message-ID: <37C18D32.5682BD9A@bc.edu> Hi Guys! I have been rather quiet lately, and this will continue for this week. I have one more exam to take on Thursday to complete my Master's in biochemistry. So, it's time to hit the books! Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Fri Aug 27 00:13:54 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] cool Message-ID: <37C61082.D0E31D54@bc.edu> Hey guys, Someone did a little write-up about Loci for the Linux Software Encyclopedia: http://stommel.tamu.edu/~baum/linuxlist/linuxlist/node30.html#Loci BTW, I took my exam, and I'm now going to get back to work on Loci. Jeers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From gvd at redpoll.pharmacy.ualberta.ca Fri Aug 27 13:31:33 1999 From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] cool In-Reply-To: <37C61082.D0E31D54@bc.edu> from "J.W. Bizzaro" at Aug 27, 99 04:13:54 am Message-ID: <199908271731.LAA01752@redpoll.pharmacy.ualberta.ca> > > Hey guys, > > Someone did a little write-up about Loci for the Linux Software Encyclopedia: > Hey that _is_ cool! > BTW, I took my exam, and I'm now going to get back to work on Loci. Kudos, I'll buy you a beer when I get into boston! =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca Faculty of Pharmacy Phone: (780) 492-4493 University of Alberta FAX: (780) 492-5305 Edmonton, Alberta, Canada From gvd at redpoll.pharmacy.ualberta.ca Fri Aug 27 15:22:04 1999 From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] rfc for loci web pages Message-ID: <199908271922.NAA02456@redpoll.pharmacy.ualberta.ca> Locians, I have a template page for the Loci pages ready for viewing http://gvd.v-wave.com/loci Its JUST a template page, so not all the links work, and I'm trying to get a couple of bugs out. Let me tell you, trying to use style sheets for positioning is a waste of time like you would not believe! So I have given up and used tables for positioning. Here is a small run down of the web page design 1. Each web page has a header file that is 'included' by php -- thats the logo. 2. The web page grabs a random background each time you reload -- very trippy! 3. Then there is a bunch of table formatting to prepare for the main content and the table of contents. 4. The file php 'includes' a trailer as well - so far just a button to the propaganda.themes page, but i'll probably put an apache logo, and maybe a loci button ! Everyone that has seen the template pages so far says they are very nice. The lambda logo is a hit with everyone-- it's basically ripped off from half-life (rocking video game) which is in turn ripped off from Aphex Twin (ambient music). You can also go to http://gvd.v-wave.com/ and there is a template page for the open lab there too, but it's no different than the loci page for all practical purposes. For fun you can navigate to the loci page from the tol main page by clicking Development projects, then The Loci Project. From there you can go the Loci development page or the GNU Lesser Public Licence link--but not all of these pages are 'sync'd yet--hopefully before the end of the week! I await your comments! --Gary =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca Faculty of Pharmacy Phone: (780) 492-4493 University of Alberta FAX: (780) 492-5305 Edmonton, Alberta, Canada From carlosm at netapp.com Fri Aug 27 15:59:36 1999 From: carlosm at netapp.com (Carlos Maltzahn) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] rfc for loci web pages In-Reply-To: <199908271922.NAA02456@redpoll.pharmacy.ualberta.ca> Message-ID: Looks nice -- but if you have a slow connection, the huge logo and the changing background can be really annoying. I prefer simple and fast web pages (e.g. www.python.org). Carlos On Fri, 27 Aug 1999, Gary Van Domselaar wrote: Locians, I have a template page for the Loci pages ready for viewing http://gvd.v-wave.com/loci Its JUST a template page, so not all the links work, and I'm trying to get a couple of bugs out. Let me tell you, trying to use style sheets for positioning is a waste of time like you would not believe! So I have given up and used tables for positioning. Here is a small run down of the web page design 1. Each web page has a header file that is 'included' by php -- thats the logo. 2. The web page grabs a random background each time you reload -- very trippy! 3. Then there is a bunch of table formatting to prepare for the main content and the table of contents. 4. The file php 'includes' a trailer as well - so far just a button to the propaganda.themes page, but i'll probably put an apache logo, and maybe a loci button ! Everyone that has seen the template pages so far says they are very nice. The lambda logo is a hit with everyone-- it's basically ripped off from half-life (rocking video game) which is in turn ripped off from Aphex Twin (ambient music). You can also go to http://gvd.v-wave.com/ and there is a template page for the open lab there too, but it's no different than the loci page for all practical purposes. For fun you can navigate to the loci page from the tol main page by clicking Development projects, then The Loci Project. From there you can go the Loci development page or the GNU Lesser Public Licence link--but not all of these pages are 'sync'd yet--hopefully before the end of the week! I await your comments! --Gary =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca Faculty of Pharmacy Phone: (780) 492-4493 University of Alberta FAX: (780) 492-5305 Edmonton, Alberta, Canada _______________________________________________ pipet-devel maillist - pipet-devel@bioinformatics.org http://bioinformatics.org/mailman/listinfo/pipet-devel From bizzaro at bc.edu Fri Aug 27 16:07:46 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] rfc for loci web pages References: <199908271922.NAA02456@redpoll.pharmacy.ualberta.ca> Message-ID: <37C6F012.A30EB6DB@bc.edu> Locians, I'm back from the dead...for now. I checked out the new Web pages a little earlier and told Gary just how groovy and far out it is. Don't you agree? BTW, Gary, you should also post that message to the main TOL mailing list: theopenlab@bioinformatics.org :-P Jeff Gary Van Domselaar wrote: > > Locians, > > I have a template page for the Loci pages ready for viewing > > http://gvd.v-wave.com/loci > > Its JUST a template page, so not all the links work, and I'm trying to > get a couple of bugs out. Let me tell you, trying to use style sheets > for positioning is a waste of time like you would not believe! So I have > given up and used tables for positioning. Here is a small run down of > the web page design > > 1. Each web page has a header file that is 'included' by php -- thats the > logo. > > 2. The web page grabs a random background each time you reload -- very > trippy! > > 3. Then there is a bunch of table formatting to prepare for the main content > and the table of contents. > > 4. The file php 'includes' a trailer as well - so far just a button to > the propaganda.themes page, but i'll probably put an apache logo, and > maybe a loci button ! > > Everyone that has seen the template pages so far says they are very nice. > The lambda logo is a hit with everyone-- it's basically ripped off from > half-life (rocking video game) which is in turn ripped off from Aphex Twin > (ambient music). > > You can also go to > > http://gvd.v-wave.com/ > > and there is a template page for the open lab there too, but it's no > different than the loci page for all practical purposes. For fun you can > navigate to the loci page from the tol main page by clicking Development > projects, then The Loci Project. From there you can go the Loci > development page or the GNU Lesser Public Licence link--but not all of > these pages are 'sync'd yet--hopefully before the end of the week! > > I await your comments! > > --Gary > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca > Faculty of Pharmacy Phone: (780) 492-4493 > University of Alberta FAX: (780) 492-5305 > Edmonton, Alberta, Canada > > _______________________________________________ > pipet-devel maillist - pipet-devel@bioinformatics.org > http://bioinformatics.org/mailman/listinfo/pipet-devel -- +--------------------------------------------------+ | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN LAB | | Bioinformatics Research, Development & Resources | | | | http://bioinformatics.org/ | +--------------------------------------------------+ From bizzaro at bc.edu Fri Aug 27 16:13:46 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] rfc for loci web pages References: Message-ID: <37C6F17A.7E01013A@bc.edu> Carlos Maltzahn wrote: > > Looks nice -- but if you have a slow connection, the huge logo and the > changing background can be really annoying. I prefer simple and fast web > pages (e.g. www.python.org). Gary, I've been using 1/4-size images from Bowie Poag's collection. I think Bowie's images are about 40 k each. I managed to get them down to < 10 k. This is where I keep them: http://bioinformatics.org/bgrounds/ I guess you're linking directly to the themes.org page; is that right? Cheerios. Jeff -- +--------------------------------------------------+ | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN LAB | | Bioinformatics Research, Development & Resources | | | | http://bioinformatics.org/ | +--------------------------------------------------+ From gvd at redpoll.pharmacy.ualberta.ca Fri Aug 27 16:44:37 1999 From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] rfc for loci web pages In-Reply-To: <37C6F17A.7E01013A@bc.edu> from "J.W. Bizzaro" at Aug 27, 99 08:13:46 pm Message-ID: <199908272044.OAA02825@redpoll.pharmacy.ualberta.ca> > > Carlos Maltzahn wrote: > > > > Looks nice -- but if you have a slow connection, the huge logo and the > > changing background can be really annoying. I prefer simple and fast web > > pages (e.g. www.python.org). I understand that sentiment, but I would also argue that people with slow connections can turn images off in the preferences section of their browser, also, I think I can use PHP to allow people to 'customize' pages so that they can have a static background, text only, etc... The Python page is simple and fast, but its not the most aesthetically pleasing web page in the world... I have also tried to keep the file sizes for the images small. The loci logo is about 48 Kb, and each background tile is between 16 and 60 Kb. The images cache, so every new page only requires a new background, so about max 60 kb overhead per page. Is this too much? I've talked to some others around the lab-- they seem to think its worth it. > > Gary, I've been using 1/4-size images from Bowie Poag's collection. I think > Bowie's images are about 40 k each. I managed to get them down to < 10 k. This > is where I keep them: > > http://bioinformatics.org/bgrounds/ > > I guess you're linking directly to the themes.org page; is that right? Actually, I went through every tile in the propaganda collection and downloaded the nice ones to the bgrounds directory (on my computer). There are 219 in the new bgrounds dir, but they havent been resized. If it is important enough, I suppose we could resize the backgrounds and logos. regards, =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca Faculty of Pharmacy Phone: (780) 492-4493 University of Alberta FAX: (780) 492-5305 Edmonton, Alberta, Canada From bizzaro at bc.edu Fri Aug 27 18:45:09 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:48 2006 Subject: [Pipet Devel] rfc for loci web pages References: <199908272044.OAA02825@redpoll.pharmacy.ualberta.ca> Message-ID: <37C714F5.9D844B79@bc.edu> Gary Van Domselaar wrote: > > Actually, I went through every tile in the propaganda collection and > downloaded the nice ones to the bgrounds directory (on my computer). Yeah, I did the same thing with my collection. I even adjusted the brightness on some so that they would not look dark. Just for kicks, you might want to compare my modified images to Bowie's originals. > There > are 219 in the new bgrounds dir, but they havent been resized. If it is > important enough, I suppose we could resize the backgrounds and logos. Well, I'll leave it up to you. I don't think it's bad the way the sizes are now. But if you're asking me what I'd do, I might make the logos 75% of their current size and use 1/4-sized backgrounds. (But 219 images?! That's a lot of resizing.) Then the browser would only be downloading ~10 kB in graphics for each page. Most modems will do that in 2 seconds. I used the GIMP to reduce the backgrounds, BTW. Check out the huge graphics that VA Linux just put up on their site: http://www.valinux.com/ For some reason, downloading the VA pages takes a lot of processing power from my CPU. Oh, and I wouldn't expect a lot of comments from the people on these lists. I know we have over 2-dozen subscribed, but sometimes only 2 or 3 get involved in the conversations. Lately it's been you, Jennifer and myself on the Loci list. But I'm sure many will take a look. WON'T YOU, GUYS? Maybe everyone's on vacation? :-) Jeff -- +--------------------------------------------------+ | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN LAB | | Bioinformatics Research, Development & Resources | | | | http://bioinformatics.org/ | +--------------------------------------------------+ From gvd at redpoll.pharmacy.ualberta.ca Fri Aug 27 18:46:18 1999 From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:18:49 2006 Subject: [Pipet Devel] rfc for loci web pages In-Reply-To: <37C714F5.9D844B79@bc.edu> from "J.W. Bizzaro" at Aug 27, 99 10:45:09 pm Message-ID: <199908272246.QAA03296@redpoll.pharmacy.ualberta.ca> > > Well, I'll leave it up to you. I don't think it's bad the way the sizes are > now. But if you're asking me what I'd do, I might make the logos 75% of their > current size... np and use 1/4-sized backgrounds. (But 219 images?! That's a lot of > resizing.) Then the browser would only be downloading ~10 kB in graphics for > each page. Most modems will do that in 2 seconds. I used the GIMP to reduce > the backgrounds, BTW. may be a prob. I'm pretty sure you can run gimp from command line. It may be possible to write a script (script-fu?) to resize the backgrounds. > > Check out the huge graphics that VA Linux just put up on their site: > > http://www.valinux.com/ > > For some reason, downloading the VA pages takes a lot of processing power from > my CPU. > Yeah mine too. From that perspective, I think our pages are pretty efficient :-) From bizzaro at bc.edu Fri Aug 27 19:12:08 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:49 2006 Subject: [Pipet Devel] rfc for loci web pages References: <199908272246.QAA03296@redpoll.pharmacy.ualberta.ca> Message-ID: <37C71B48.30A710E8@bc.edu> Gary Van Domselaar wrote: > > may be a prob. I'm pretty sure you can run gimp from command line. It may > be possible to write a script (script-fu?) to resize the backgrounds. I just looked in the bgrounds directory. Dang, Bowie makes some purdy pictures! I tell you what, if you can put all those in a tarball in the same directory, I'll download them and take a crack at resizing them. Maybe with PHP we can have the option to get the backgrounds from bg-large or bg-small directories. :-D Jeff -- +--------------------------------------------------+ | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN LAB | | Bioinformatics Research, Development & Resources | | | | http://bioinformatics.org/ | +--------------------------------------------------+ From stein at fmppr.fmnh.org Fri Aug 27 19:36:04 1999 From: stein at fmppr.fmnh.org (JES) Date: Fri Feb 10 19:18:49 2006 Subject: [Pipet Devel] rfc for loci web pages References: <199908272246.QAA03296@redpoll.pharmacy.ualberta.ca> <37C71B48.30A710E8@bc.edu> Message-ID: <37C720E4.75B978@fmnh.org> Looks purty... My speedy work machine (but slow T1) spews forth the images just fine... a little slower than I would normally like, but better than some sites I've seen recently. The real test comes when I use my lowly pentium 133 at home over ISDN - home dirs mounted from a pentium 90 that complains about buffer overflows. I usually have little patience for slow-loading sites... but then Phil has imprinted his web style on me (http://alloy.net). -j -------------------------- Jennifer Steinbachs, PhD Computational Biologist Dept. of Botany The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 email: stein@fmnh.org -------------------------- From bizzaro at bc.edu Tue Aug 31 19:11:07 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:49 2006 Subject: [Pipet Devel] PSB 2000 References: <37B2B7C9.566D465@bc.edu> <37B2F9ED.481F9176@fmnh.org> <37B300B7.DBD7DFE5@bc.edu> Message-ID: <37CC610B.D84420C4@bc.edu> GOING TO PSB 2000 YES MAYBE NO NO REPLY ---------------------------------------------------------------------- Bizzaro Junier Williams Triche Van Domselaar St. Onge Harrison Cohen Steinbachs Rice Lapointe Villa Beck Mangalam Zuazaga Bradford Harrison Marx Hinsen Jain de Lahondes Sicheritz Please update this list as needed. BTW, my brother got a package deal from his travel agent: $670 per ticket (I think that's from Chicago) INCLUDES RENTAL CAR! Compare that to the group rate via United: $1,014 per ticket (from Boston) (no car) :-P Jeff -- +--------------------------------------------------+ | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN LAB | | Bioinformatics Research, Development & Resources | | | | http://bioinformatics.org/ | +--------------------------------------------------+ From bizzaro at bc.edu Tue Aug 31 20:50:02 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:49 2006 Subject: [Pipet Devel] LOCI '99 Message-ID: <37CC783A.FF87230F@bc.edu> Locians, This message is from Gary. I thought I'd share it with this list (this is 'The Open Lab' afterall). It's about the upcoming (mid-September) Loci meeting in Boston (LOCI '99). The meeting will be pretty small (4-5 people) and short (2 hours). If you will be in the area and would like to attend, let me know. Otherwise, there is no need to travel any great distance. The most likely attendees are: Gary Van Domselaar Ken Marx David Lapointe Me Justin, Humberto and Alan, who have been contributing to the design of Loci's underpinnings: WE NEED MORE FEEDBACK! The concept is complete, but the implementation is not. We left off this summer talking about CORBA, DOM and 'Data Managers', but then everything went silent. We need to get these things ironed out for presentations, publications and grant proposals. See below. Thus spaketh Gary: ------------- There are several of us who will be in Boston from in September from the 7th to the 21st. I was thinking we should perhaps have an initial agenda of issues that we would like to cover while we are down there, so we could perhaps prep a bit ahead of time (although prep time is running short!). Any ideas? I was thinking: 0. Review the status of the Loci project as it currently stands, in terms of active developers and advisors. Perhaps we should plan recruiting strategy to attract more developers. We should set milestone dates as well for the different aspects of Loci development, although I understand that with volunteer grad students as developers, these milestones are basically pipe-dreams, but granting agencies like to see them ;-) 1. Formalize the project details. This will take a collaboration between our resident experts, Justin, Humberto, etc. With their input, I think Jeff and I may be able to draft something and identify which parts of loci are still sketchy and need to be fleshed-out, so that we can begin the process of writing a grant application. This, I imagine, may take quite a bit of time. 2. Identify granting agencies and programs under which our project may fit. Has anyone looked into GNU? I understand that they can offer resources for gpl development, ie web space. 3. Identify popular micro-breweries in Boston and evaluate them ;-). ------------- :-b Jeff -- +--------------------------------------------------+ | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN LAB | | Bioinformatics Research, Development & Resources | | | | http://bioinformatics.org/ | +--------------------------------------------------+