From mark.schreiber at novartis.com Wed Apr 13 23:30:50 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Wed Apr 13 23:24:29 2005 Subject: [Biojava-dev] missing docbook file Message-ID: Hello Cary, This reference should be removed from the ant build script. I think that the docbook section is no longer being maintained and is out of date. As such it should be removed from CVS and all later versions of biojava. If no one has any complaints I will do this soon. - Mark Cary Scofield Sent by: biojava-dev-bounces@portal.open-bio.org 03/04/2005 10:54 PM To: biojava-dev@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] missing docbook file Hello, I have the source to biojava-1.4pre1 and when I tried to execute the ant target "docbook", it complained that it could not find biojava-doc-main.xml file. If anyone has this file, could you please email it to me. Thanks, Cary Scofield ===== Cary Scofield carys689@yahoo.com cps0@labs.gte.com __________________________________ Celebrate Yahoo!'s 10th Birthday! Yahoo! Netrospective: 100 Moments of the Web http://birthday.yahoo.com/netrospective/ _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From mark.schreiber at novartis.com Wed Apr 13 23:33:34 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Wed Apr 13 23:27:15 2005 Subject: [Biojava-dev] Inheriting from the HMM classes Message-ID: I will have a look at this shortly. >From a quick look at your code it seems that most changes are making private methods protected. I think this should mostly be OK. Thanks for the suggestions, Mark Lukas Kall Sent by: biojava-dev-bounces@portal.open-bio.org 02/22/2005 11:09 PM To: biojava-dev@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] Inheriting from the HMM classes Hi, I have tried to use the BioJava library for implementing some HMM decoding algorithms. It was fairly convenient to do so, apart from that many of the declarations in your classes are private, when I would prefer them to be public. Any chance that you could change the declarations in future versions? I have attached a diff to my sources beneath. Meanwhile I have put my version under GPL (See http://phobius.cgb.ki.se/data.html). I hope that this suites you. BRs -Lukas K?ll Center for Genomics and Bioinformatics Karolinska Institutet S-171 77 Stockholm, Sweden Tel: +46 (0)8 52 48 66 88 Fax: +46 (0)8 33 79 83 http://phobius.cgb.ki.se/ diff -r biojava-1.30/src/org/biojava/bio/dp/onehead/DPCursor.java orig/biojava-1.30/src/org/biojava/bio/dp/onehead/DPCursor.java 33c33 < public interface DPCursor { --- > interface DPCursor { diff -r biojava-1.30/src/org/biojava/bio/dp/onehead/SingleDP.java orig/biojava-1.30/src/org/biojava/bio/dp/onehead/SingleDP.java 42,44c42,44 < protected final HashMap emissionsProb; < protected final HashMap emissionsOdds; < protected final HashMap emissionsNull; --- > private final HashMap emissionsProb; > private final HashMap emissionsOdds; > private final HashMap emissionsNull; 100,105c100 < double emS = scoreType.calculateScore(dis, sym); < if (emS>0.0) { < em[i] = Math.log(emS); < } else { < em[i] = Double.NEGATIVE_INFINITY; < } --- > em[i] = Math.log(scoreType.calculateScore(dis, sym)); 212c207 < protected double forward(DPCursor dpCursor, ScoreType scoreType) --- > private double forward(DPCursor dpCursor, ScoreType scoreType) 219c214 < protected double backward(DPCursor dpCursor, ScoreType scoreType) --- > private double backward(DPCursor dpCursor, ScoreType scoreType) 226c221 < protected void forward_initialize(DPCursor dpCursor, ScoreType scoreType) --- > private void forward_initialize(DPCursor dpCursor, ScoreType scoreType) 276d270 < // System.out.println("currentCol[" + states[l].getName() + "]=" + currentCol[l]); 280c274 < protected void backward_initialize(DPCursor dpCursor, ScoreType scoreType) --- > private void backward_initialize(DPCursor dpCursor, ScoreType scoreType) 294c288 < protected void forward_recurse(DPCursor dpCursor, ScoreType scoreType) --- > private void forward_recurse(DPCursor dpCursor, ScoreType scoreType) 308c302 < // System.out.println("Consuming " + sym.getName()); --- > // System.out.println("Consuming " + sym.getName()); 314c308 < // System.out.println("* at " + states[l].getName()); --- > // System.out.println("*"); 335,336c329 < if (lastCol[k] != Double.NEGATIVE_INFINITY && < lastCol[k] != Double.NaN) { --- > if (lastCol[k] != Double.NEGATIVE_INFINITY) { 339,342c332,335 < // if(states[l]== getModel().magicalState()) { < // System.out.print("magic " + "lastCol["+states[k].getName()+"]=" + lastCol[k] + " , "); < // System.out.println("t=" + t); < // } --- > if(states[l]== getModel().magicalState()) { > // System.out.print("magic " + "lastCol[k]=" + lastCol[k] + " , "); > // System.out.println("t=" + t); > } 346,349c339 < if (lastCol[k] == Double.NaN) { < System.out.println("k=" + states[k].getName() + "->l=" + states[l].getName()); < System.out.println("-"); < } --- > // System.out.println("-"); 354,359d343 < if ((new Double(currentCol[l])).isNaN()) { < System.out.println("currentCol[" + states[l].getName() + "]=" + currentCol[l]); < System.out.println("weight="+weight+", score="+score+ < ", constant="+constant); < currentCol[l]=Double.NEGATIVE_INFINITY; < } 362d345 < // System.out.println("currentCol[" + states[l].getName() + "]=" +currentCol[l]+" NaN=" + ( (new Double(currentCol[l])).isNaN())); 364,369c347,352 < /* if(states[l] == getModel().magicalState()) { < System.out.print("magic\t"); < System.out.print("Weight " + weight + "\t"); < System.out.print(", score " + score + " = " + Math.log(score) + "\t"); < System.out.println(", constant " + constant); < } */ --- > if(states[l] == getModel().magicalState()) { > // System.out.print("magic\t"); > //System.out.print("Weight " + weight + "\t"); > // System.out.print(", score " + score + " = " + Math.log(score) + "\t"); > // System.out.println(", constant " + constant); > } 393c376 < && currentCol[k] != Double.NaN --- > && currentCol[k] !=Double.NaN 398,400d380 < if (currentCol[k] == Double.NaN) { < System.out.println("k=" + states[k].getName() + "->l=" + states[l].getName()); < } 403,408c383,384 < if (score>=0.0 && score != Double.NaN) { < currentCol[l] = Math.log(score) + constant; < } else { < currentCol[l] = Double.NEGATIVE_INFINITY; < } < // System.out.println("currentCol[" + states[l].getName() + "]=" + currentCol[l]); --- > currentCol[l] = Math.log(score) + constant; > //System.out.println("currentCol[" + states[l].getName() + "]=" + currentCol[l]); 413c389 < protected void backward_recurse(DPCursor dpCursor, ScoreType scoreType) --- > private void backward_recurse(DPCursor dpCursor, ScoreType scoreType) 484c460 < protected double forward_termination(DPCursor dpCursor, ScoreType scoreType) --- > private double forward_termination(DPCursor dpCursor, ScoreType scoreType) 496c472 < protected double backward_termination(DPCursor dpCursor, ScoreType scoreType) --- > private double backward_termination(DPCursor dpCursor, ScoreType scoreType) 515c491 < protected StatePath viterbi(DPCursor dpCursor, ScoreType scoreType) --- > private StatePath viterbi(DPCursor dpCursor, ScoreType scoreType) diff -r biojava-1.30/src/org/biojava/bio/dp/onehead/SingleDPMatrix.java orig/biojava-1.30/src/org/biojava/bio/dp/onehead/SingleDPMatrix.java 36,40c36,40 < protected final State [] states; < protected final MarkovModel model; < protected final SymbolList [] symList; < public final double [][] scores; // [symbol][state] < protected double score; --- > private final State [] states; > private final MarkovModel model; > private final SymbolList [] symList; > public final double [][] scores; // [symbol][state] > private double score; 58c58 < public void setScore(double score) { --- > void setScore(double score) { diff -r biojava-1.30/src/org/biojava/bio/dp/onehead/SmallCursor.java orig/biojava-1.30/src/org/biojava/bio/dp/onehead/SmallCursor.java 34c34 < public class SmallCursor extends AbstractCursor { --- > class SmallCursor extends AbstractCursor { diff -r biojava-1.30/src/org/biojava/bio/seq/io/FastaFormat.java orig/biojava-1.30/src/org/biojava/bio/seq/io/FastaFormat.java 61c61 < protected Vector mListeners = new Vector(); --- > private Vector mListeners = new Vector(); 66c66 < protected int lineWidth = 60; --- > private int lineWidth = 60; _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From mark.schreiber at novartis.com Wed Apr 13 23:38:02 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Wed Apr 13 23:31:38 2005 Subject: [Biojava-dev] Microarray modules Message-ID: Hello - Apologies no one replied earlier. We are always keen on new submissions. Preferably they would be well documented and with tests. Having a demo available that can go on the Biojava in Anger page would also be nice. There have been on and off discussions about microarray stuff in the past. I know Michael has an interest in this. Michael, would you be willing to coordinate microarray development? Regards, Mark Tiago Lopes Sent by: biojava-dev-bounces@portal.open-bio.org 02/23/2005 07:26 PM To: biojava-dev@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] Microarray modules Hello, I hope everything is okay with you and your projects. Well, I have developes java classes for microarray analysis, and the modules are for background correction, normalization (global), and analysis by the SAM (Significance Analysis of Microarray - Tusher et al.). I want to make this classes avaliable, and I would be proud to help in the development of Biojava.org. I have wrote once, but had no answer if I could join the project or not. So, I'm writing again ! Thanks ! "Publish or perish !" ========================= Tiago Jos? da Silva Lopes ICQ: 195209391 ========================= --------------------------------- Yahoo! Acesso Gr?tis - Internet r?pida e gr?tis. Instale o discador do Yahoo! agora. _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From mark.schreiber at novartis.com Thu Apr 14 03:06:32 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Thu Apr 14 03:00:18 2005 Subject: [Biojava-dev] WG: pI Calculation in BioJava Message-ID: Not sure, I would reccomend consulting the source code for the specific calculation. - Mark "Nkemdilim Uwaje" Sent by: biojava-dev-bounces@portal.open-bio.org 03/23/2005 10:39 PM To: cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] WG: pI Calculation in BioJava Hi there, I am currently writing my thesis and would like to use the pI Calculation method of BioJava. I would like to know what algorithm it is based on, as my main aim is to compare different algorithms of pI - calculations, in order to find the best one that correlates with my experimental pI's. Thank you very much in advance N. Uwaje _______________________________________ Nkemdilim Uwaje Affectis AG Tel: +49 (0) 89 30622-434 Make visible what, without you, might never have been seen. _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From td2 at sanger.ac.uk Thu Apr 14 09:24:47 2005 From: td2 at sanger.ac.uk (Thomas Down) Date: Thu Apr 14 09:20:29 2005 Subject: [Biojava-dev] Re: [Biojava-l] Location output In-Reply-To: <1113482617.425e657936980@maili.uku.fi> References: <1113476300.425e4ccc1898e@maili.uku.fi> <1113482617.425e657936980@maili.uku.fi> Message-ID: <811b344ca97e72058f975b498d0c1e9e@sanger.ac.uk> On 14 Apr 2005, at 13:43, mmatilai@hytti.uku.fi wrote: > Hi, > > Below is the stack trace. I actually imported the RangeLocation class > to my program project so I don't > know if this should affect something. The code is the same and I still > called it RangeLocation. > > Error occurred. > java.lang.ClassCastException > at > org.biojava.bio.seq.io.AbstractGenEmblFileFormer.formatLocationBlock(Ab > stractGenEmblFileFormer.java > :647) Java classes are identified by their fully qualified names, so your.app.RangeLocation isn't considered to be interchangeable with org.biojava.bio.symbol.RangeLocation. This seems to have triggered a bug in the Genbank (and EMBL) file-writing code, which couldn't handle any Location implementation outside the core set included in the BioJava library. I've now fixed the Genbank-writing bug, so if you use the latest version from CVS, everything should work as expected. An alternative solution would be to make your custom RangeLocation a subclass of BioJava's built-in RangeLocation class: public class MyRangeLocation extends RangeLocation { public MyRangeLocation(int min, int max) { super(min, max); } public String toString() { return "" + getMin() + "," + getMax(); } } Thomas From aldaihani at hotmail.co.uk Sun Apr 17 17:08:02 2005 From: aldaihani at hotmail.co.uk (badr al-daihani) Date: Sun Apr 17 17:01:34 2005 Subject: [Biojava-dev] UniGene In-Reply-To: Message-ID: would you please tell me how to retrieve the unigene number of a gene(UniGene) knowing the GenBank accession number ? Best regards Badr _________________________________________________________________ Use MSN Messenger to send music and pics to your friends http://www.msn.co.uk/messenger From Russell.Smithies at agresearch.co.nz Sun Apr 17 18:22:50 2005 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Sun Apr 17 18:16:44 2005 Subject: [Biojava-dev] UniGene Message-ID: You can get the gene ID number using eutils: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&re tmode=text&rettype=xml&term=NM_003234 Russell Smithies Bioinformatics Software Developer AgResearch Invermay New Zealand -----Original Message----- From: biojava-dev-bounces@portal.open-bio.org [mailto:biojava-dev-bounces@portal.open-bio.org] On Behalf Of badr al-daihani Sent: Monday, 18 April 2005 9:08 a.m. To: biojava-dev@biojava.org Subject: [Biojava-dev] UniGene would you please tell me how to retrieve the unigene number of a gene(UniGene) knowing the GenBank accession number ? Best regards Badr _________________________________________________________________ Use MSN Messenger to send music and pics to your friends http://www.msn.co.uk/messenger _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber at novartis.com Sun Apr 17 21:04:01 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Sun Apr 17 20:57:38 2005 Subject: [Biojava-dev] fork tests? Message-ID: Hello - Can anyone tell me how I should use the fork-tests target in the ANT build script? Do I need to edit it to specify the packages I want to test? Thanks, Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From td2 at sanger.ac.uk Mon Apr 18 04:02:51 2005 From: td2 at sanger.ac.uk (Thomas Down) Date: Mon Apr 18 03:56:22 2005 Subject: [Biojava-dev] fork tests? In-Reply-To: References: Message-ID: <14a78e7642f3b641172baa53b7531ac3@sanger.ac.uk> On 18 Apr 2005, at 02:04, mark.schreiber@novartis.com wrote: > Hello - > > Can anyone tell me how I should use the fork-tests target in the ANT > build > script? Do I need to edit it to specify the packages I want to test? Do you mean the runtests-fork target? Should work in exactly the same way as the normal "runtests" target, except that it's much, much, slower because it starts a new Java process for every test. Thomas. From mark.schreiber at novartis.com Mon Apr 18 04:05:21 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Mon Apr 18 03:58:52 2005 Subject: [Biojava-dev] fork tests? Message-ID: So why would one use runtests-fork? (or is runtests the slow one)? - Mark Thomas Down 04/18/2005 04:02 PM To: Mark Schreiber/GP/Novartis@PH cc: biojava-dev@biojava.org, matthew.pocock@ncl.ac.uk Subject: Re: [Biojava-dev] fork tests? On 18 Apr 2005, at 02:04, mark.schreiber@novartis.com wrote: > Hello - > > Can anyone tell me how I should use the fork-tests target in the ANT > build > script? Do I need to edit it to specify the packages I want to test? Do you mean the runtests-fork target? Should work in exactly the same way as the normal "runtests" target, except that it's much, much, slower because it starts a new Java process for every test. Thomas. From smh1008 at cam.ac.uk Mon Apr 11 19:05:28 2005 From: smh1008 at cam.ac.uk (David Huen) Date: Mon Apr 18 22:45:09 2005 Subject: [Biojava-dev] WG: pI Calculation in BioJava In-Reply-To: References: Message-ID: I implemented the original version in Biojava but I don't know if it is still the same one being used. The original just used the pKa's of the amino acids and computed the pI by assuming that each AA ionised independently of the others. The pI was the pH at which the next charge was zero. The pKa's used were the same as those used in GCG. From robinxml at yahoo.com Sat Apr 16 07:23:21 2005 From: robinxml at yahoo.com (Robin XML) Date: Mon Apr 18 22:45:10 2005 Subject: [Biojava-dev] XML format Message-ID: <20050416112322.25747.qmail@web30114.mail.mud.yahoo.com> Dear All, Please help! I am a beginner in bioJava. Is it possible to retrieve data from GenBank or SwissProt by access ID, and then transfer to XML format? Thank you!!!!!! Best regards, Robin > __________________________________ Do you Yahoo!? Yahoo! Mail - now with 250MB free storage. Learn more. http://info.mail.yahoo.com/mail_250 From mark.schreiber at novartis.com Mon Apr 18 22:55:17 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Mon Apr 18 22:49:40 2005 Subject: [Biojava-dev] XML format Message-ID: You can use NCBI's eutils to get GenBank in XML format. BioJava has a GenBankXML parser. Robin XML Sent by: biojava-dev-bounces@portal.open-bio.org 04/16/2005 07:23 PM To: biojava-l@biojava.org cc: biojava-dev@biojava.org, (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] XML format Dear All, Please help! I am a beginner in bioJava. Is it possible to retrieve data from GenBank or SwissProt by access ID, and then transfer to XML format? Thank you!!!!!! Best regards, Robin > __________________________________ Do you Yahoo!? Yahoo! Mail - now with 250MB free storage. Learn more. http://info.mail.yahoo.com/mail_250 _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From Russell.Smithies at agresearch.co.nz Mon Apr 18 22:58:25 2005 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon Apr 18 22:51:48 2005 Subject: [Biojava-dev] XML format Message-ID: Use eutils Here's an example: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&i d=NM_003234&report=docsum&rettype=xml Russell -----Original Message----- From: biojava-dev-bounces@portal.open-bio.org [mailto:biojava-dev-bounces@portal.open-bio.org] On Behalf Of Robin XML Sent: Saturday, 16 April 2005 11:23 p.m. To: biojava-l@biojava.org Cc: biojava-dev@biojava.org Subject: [Biojava-dev] XML format Dear All, Please help! I am a beginner in bioJava. Is it possible to retrieve data from GenBank or SwissProt by access ID, and then transfer to XML format? Thank you!!!!!! Best regards, Robin > __________________________________ Do you Yahoo!? Yahoo! Mail - now with 250MB free storage. Learn more. http://info.mail.yahoo.com/mail_250 _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From Russell.Smithies at agresearch.co.nz Mon Apr 18 23:00:34 2005 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon Apr 18 22:53:53 2005 Subject: [Biojava-dev] XML format Message-ID: Sorry, here's the XML version: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&i d=NM_003234&rettype=gb&retmode=text -----Original Message----- From: biojava-dev-bounces@portal.open-bio.org [mailto:biojava-dev-bounces@portal.open-bio.org] On Behalf Of Robin XML Sent: Saturday, 16 April 2005 11:23 p.m. To: biojava-l@biojava.org Cc: biojava-dev@biojava.org Subject: [Biojava-dev] XML format Dear All, Please help! I am a beginner in bioJava. Is it possible to retrieve data from GenBank or SwissProt by access ID, and then transfer to XML format? Thank you!!!!!! Best regards, Robin > __________________________________ Do you Yahoo!? Yahoo! Mail - now with 250MB free storage. Learn more. http://info.mail.yahoo.com/mail_250 _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From dlondon at ebi.ac.uk Tue Apr 19 05:16:30 2005 From: dlondon at ebi.ac.uk (Darin London) Date: Tue Apr 19 07:05:22 2005 Subject: [Biojava-dev] Re: BOSC 2005 In-Reply-To: <20050120175859.GA7254@parrot.ebi.ac.uk> References: <20050120175859.GA7254@parrot.ebi.ac.uk> Message-ID: <20050419091628.GN17377@parrot.ebi.ac.uk> {Please pass the word!} SECOND CALL FOR SPEAKERS The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 13th International Conference on Intelligent Systems for Molecular Biology. see http://www.iscb.org/ismb2005 for more information. Because of the power of many Open Source bioinformatics packages in use by the Research Community today, it is not too presumptuous to say that the work of the Open Source Bioinformatics Community represents the cutting edge of Bioinformatics in general. This has been repeatedly demonstrated by the quality of presentations at previous BOSC conferences. This year, at BOSC 2005, we want to continue this tradition of excellence, while presenting this message to a wider part of the Research Community. Please, pass this message on to anyone you know that is interested in Bioinformatics software. BOSC PROGRAM & CONTACT INFO * Web: http://www.open-bio.org/bosc2005/ * Online Registration: https://www.cteusa.com/iscb4/ * Email: bosc@open-bio.org FEES * Corporate : $195 ($245 after May 16th) * Academic : $170 ($220 after May 16th) * Student : $145 ($195 after May 16th) SPEAKERS & ABSTRACTS WANTED The program committee is currently seeking abstracts for talks at BOSC 2005. BOSC is a great opportunity for you to tell the community about your use, development, or philosophy of open source software development in bioinformatics. The committee will select several submitted abstracts for 25-minute talks and others for shorter "lightning" talks. Accepted abstracts will be published on the BOSC web site. If you are interested in speaking at BOSC 2005, please send us before April 26, 2005: * an abstract (no more than a few paragraphs) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. Abstracts will be accepted for submission until April 26, 2005. Abstracts chosen for presentation will be announced May 12, 2005 (before the ISMB Early Registration Deadline). LIGHTNING-TALK SPEAKERS WANTED! The program committee is currently seeking speakers for the lightning talks at BOSC 2005. Lightning talks are quick - only five minutes long - and a great opportunity for you to give people a quick summary of your open source project, code, idea, or vision of the future. If you are interested in giving a lightning talk at BOSC 2005, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. We will accept entries on-line until BOSC starts, but space for demos and lightning talks is limited.
(sorry for multiple postings, but please do forward to anyone else who you think might be interested) ------------------------------------------------------------------------ ----------- Dear everyone, It has been a long time and we Bioinformatics devotees are overdue for another total-immersion coding-fest (the last hackathon was held in Singapore February 2003, more than two years ago). Apple has offered to host us this year, and as an added bonus include free admission to the World-Wide Developers Conference in San Francisco the prior week. They are also looking for some people to present interesting new developments at the WWDC, so if you have something noteworthy please let us know. Apple is not attaching any strings, so our work need not address Apple-specific software or hardware areas. Apple will provide space and hardware (and access to their engineers if we'd like). Week 1 (June 6-10) would be spent at the WWDC. Week 2 (June 12-16) would be in Cupertino, at Apple's headquarters. We're free to focus on what interests us, our tentative plans include: 1. Bio-ontologies software 2. High-performance computing (e.g. large scale computations, optimization) 3. Image analysis 4. Documentation 5. Anything else that may interest you Our plan is to organize this much as the Aspen Center for Physics computational biology workshops were organized (for those old enough to remember): A couple of presentations to start the day; collaboration and coding afterwards; time for a bit of fun (does anyone else cycle?), and discussions in the late afternoons and evenings. Would everyone who is interested in attending please send us a short description of what you would like to do, and perhaps other people who you would like to work with. There is somewhat limited space, so we will try to prioritize groups that have a clear focus and a need to interact. We now this is very short notice, but we hope that there will be enough interest to make it possible. We are looking into additional funding support, to pay for travel expenses, but this is still to be decided. Looking forward to hearing from everyone. George, Cyrus, Steve, and Suzanna (the Bay Area locals)