From andreas at sdsc.edu Sun Mar 3 14:49:57 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 3 Mar 2013 11:49:57 -0800 Subject: [Biojava-l] GSoC 2013 is ON Message-ID: Hi, Pjotr Prins will be the GSoC project administrator for the Open Bioinformatics Foundation this year. I am passing along his message about this year's organisation and deadlines: Game on! GSoC 2013 is ON. I am running with the OBF project administration this year for the Google Summer of code (GSoC). First and foremost I want to thank Robert Buels and others for making OBF/GSoC a success in the previous three years! This year, Robert, Chris Fields and Hilmar Lapp will act as backup administrators. The deadline for the OBF application for GSoC2013 as a mentoring organisation is Friday March 29! See http://www.google-melange.com/gsoc/events/google/gsoc2013 Similar to previous years, each Bio* project needs to update and add project ideas on the project's individual OBF wiki page and create links from the main OBF page at http://www.open-bio.org/wiki/Google_Summer_of_Code (we will update the main information on that page soon). So, for each of the OBF projects that wants to do GSoC again this year: 1. Update the list of project ideas on your project's GSoC page (BioPython, BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done or no longer relevant, etc. For an example see http://bioruby.open-bio.org/wiki/Google_Summer_of_Code 2. Update the final list of project ideas on the main OBF GSoC page to match. http://www.open-bio.org/wiki/Google_Summer_of_Code 3. Register with gsoc at lists.open-bio.org 4. Announce it on that list when you are ready :) Anyone can submit a project idea! Former GSoC students are especially encouraged to contribute ideas to the mailing lists. Please have the updates done by Friday March 22nd. The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organisation again this year, so let's come up with some good ones! Pj. (Pjotr Prins) Important dates: * March 22nd: Finalise project ideas * March 29th: Deadline OBF mentoring organisation submission to Google http://www.open-bio.org/wiki/Google_Summer_of_Code From chrisrogersrogers at aol.com Wed Mar 13 14:35:28 2013 From: chrisrogersrogers at aol.com (chrisrogersrogers at aol.com) Date: Wed, 13 Mar 2013 14:35:28 -0400 (EDT) Subject: [Biojava-l] WORLDCOMP Strikes Again for the Last Time Message-ID: <8CFEE30AAB5884A-708-1310C@Webmail-d108.sysops.aol.com> I graduated from University of Florida (UFL) and am currently running a computer firm in Florida. I have attended WORLDCOMP http://www.world-academy-of-science.org in 2010. Except for few keynote speeches and presentations, the conference was very disappointing due to a large number of poor quality papers and cancellation of some sessions. I was instantly suspicious of this conference. Me and my UFL and UGA friends started a study on WORLDCOMP. We submitted a paper to WORLDCOMP 2011 and again (the same paper with a modified title) to WORLDCOMP 2012. This paper had numerous fundamental mistakes. Sample statements from that paper include: (1). Binary logic is fuzzy logic and vice versa (2). Pascal developed fuzzy logic (3). Object oriented languages do not exhibit any polymorphism or inheritance (4). TCP and IP are synonyms and are part of OSI model (5). Distributed systems deal with only one computer (6). Laptop is an example for a super computer (7). Operating system is an example for computer hardware Also, our paper did not express any conceptual meaning. However, it was accepted both the times without any modifications (and without any reviews) and we were invited to submit the final paper and a payment of $500+ fee to present the paper. We decided to use the fee for better purposes than making Prof. Hamid Arabnia (Chairman of WORLDCOMP) rich. After that, we received few reminders from WORLDCOMP to pay the fee but we never responded. We MUST say that you should look at the website http://sites.google.com/site/worlddump1 if you have any thoughts to submit a paper to WORLDCOMP. DBLP and other indexing agencies have stopped indexing WORLDCOMP?s proceedings since 2011 due to its fakeness. The status of your WORLDCOMP papers can be changed from ?scientific? to ?other? (i.e., junk or non-technical) at anytime. See the comments http://www.mail-archive.com/tccc at lists.cs.columbia.edu/msg05168.html of a respected researcher on this. Better not to have a paper than having it in WORLDCOMP and spoil the resume and peace of mind forever! Our study revealed that WORLDCOMP is a money making business, using UGA mask, for Prof. Hamid Arabnia. He is throwing out a small chunk of that money (around 20 dollars per paper published in WORLDCOMP?s proceedings) to his puppet who publicizes WORLDCOMP and also defends it at various forums, using fake/anonymous names. The puppet uses fake names and defames other conferences/people to divert traffic to WORLDCOMP. That is, the puppet does all his best to get a maximum number of papers published at WORLDCOMP to get more money into his (and Prof. Hamid Arabnia?s) pockets. Monte Carlo Resort (the venue of WORLDCOMP until 2012) has refused to provide the venue for WORLDCOMP?13 because of the fears of their image being tarnished due to WORLDCOMP?s fraudulent activities. WORLDCOMP will not be held after 2013. The paper submission deadline for WORLDCOMP?13 is March 18, 2013 (it will be extended many times, as usual) but still there are no committee members, no reviewers, and there is no conference Chairman. The only contact details available on WORLDCOMP?s website is just an email address! What bothers us the most is that Prof. Hamid Arabnia never posted an apology for the damage he has done to the research community. He is still trying to defend WORLDCOMP. Let us make a direct request to him: publish all reviews for all the papers (after blocking identifiable details) since 2000 conference. Reveal the names and affiliations of all the reviewers (for each year) and how many papers each reviewer had reviewed on average. We also request him to look at the Open Challenge at http://sites.google.com/site/dumpconf We think that it is our professional obligation to spread this message to alert the computer science community. Sorry for posting to multiple lists. Spreading the word is the only way to stop this bogus conference. Please forward this message to other mailing lists and people. We are shocked with Prof. Hamid Arabnia and his puppet?s activities http://worldcomp-fake-bogus.blogspot.com Search Google using the keywords ?worldcomp, fake? for additional links. Sincerely, Chris From jjramirez at estudiantes.uci.cu Tue Mar 19 11:52:33 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Tue, 19 Mar 2013 11:52:33 -0400 (EDT) Subject: [Biojava-l] Drawing chromatogram from ab1 file Message-ID: <7ee1c876-6b74-4385-928d-773c737cec97@ucimail4.uci.cu> Hello comunity I have some ab1 files and I need to draw the chromatogram usin biojava, already got the sequence, but now I need show the chromatogram. Somebody know the code to do this ? thanks for you time. Janier -- Universidad de las Ciencias Inform?ticas Janier J. Ram?rez Landaburo Facultad - 6 Tel-837-3121 From ngsbioinformatics at gmail.com Tue Mar 19 13:56:02 2013 From: ngsbioinformatics at gmail.com (Ryan Golhar) Date: Tue, 19 Mar 2013 13:56:02 -0400 Subject: [Biojava-l] Drawing chromatogram from ab1 file In-Reply-To: <7ee1c876-6b74-4385-928d-773c737cec97@ucimail4.uci.cu> References: <7ee1c876-6b74-4385-928d-773c737cec97@ucimail4.uci.cu> Message-ID: There are lots of programs available to do this. I have a Java program at http://github.com/golharam/ChromViewer that does this as well. On Tue, Mar 19, 2013 at 11:52 AM, Janier J. Ram?rez < jjramirez at estudiantes.uci.cu> wrote: > Hello comunity > > I have some ab1 files and I need to draw the chromatogram usin biojava, > already got the sequence, but now I need show the chromatogram. > Somebody know the code to do this ? > > thanks for you time. > > Janier > -- > > > Universidad de las Ciencias Inform?ticas > Janier J. Ram?rez Landaburo > Facultad - 6 > Tel-837-3121 > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From wzhao6898 at gmail.com Wed Mar 20 17:09:03 2013 From: wzhao6898 at gmail.com (wzhao6898 at gmail.com) Date: Wed, 20 Mar 2013 14:09:03 -0700 Subject: [Biojava-l] (no subject) Message-ID: Hi there, Maybe this has been discussed before, but where can I find the proteomic package that was in version 1.8.2? Thanks, DZ From wzhao6898 at gmail.com Wed Mar 20 17:10:03 2013 From: wzhao6898 at gmail.com (wzhao6898 at gmail.com) Date: Wed, 20 Mar 2013 14:10:03 -0700 Subject: [Biojava-l] Proteomic package in Biojava 3 Message-ID: Hi there, Maybe this has been discussed before, but where can I find the proteomic package that was in version 1.8.2? Thanks, DZ From andreas at sdsc.edu Wed Mar 20 18:33:23 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 20 Mar 2013 15:33:23 -0700 Subject: [Biojava-l] Proteomic package in Biojava 3 In-Reply-To: References: Message-ID: Hi, what functionality do you need exactly? There are several new modules in biojava 3 that contain related functionality. Probably the closest might be *biojava3-aa-prop *Physico chemial properties: http://biojava.org/wiki/BioJava:CookBook#Physico-Chemical_Properties_Computation Is this what you need? Andreas On Wed, Mar 20, 2013 at 2:10 PM, wzhao6898 at gmail.com wrote: > Hi there, > > Maybe this has been discussed before, but where can I find the > proteomic package that was in version 1.8.2? > Thanks, > > DZ > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From andreas at sdsc.edu Wed Mar 20 18:46:46 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 20 Mar 2013 15:46:46 -0700 Subject: [Biojava-l] Proteomic package in Biojava 3 In-Reply-To: References: Message-ID: I think Digest and related classes have not been migrated to biojava 3 as of yet. However that code for digesting sequences seems quite independent and should be easy to migrate that over to biojava 3.... Andreas On Wed, Mar 20, 2013 at 3:40 PM, wzhao6898 at gmail.com wrote: > Thanks for the reply, I'm actually interested in the Digest and related > classes. > > DZ > > On Wed, Mar 20, 2013 at 3:33 PM, Andreas Prlic wrote: > > Hi, > > > > what functionality do you need exactly? There are several new modules in > > biojava 3 that contain related functionality. Probably the closest might > be > > > > biojava3-aa-prop Physico chemial properties: > > > > > http://biojava.org/wiki/BioJava:CookBook#Physico-Chemical_Properties_Computation > > > > Is this what you need? > > > > Andreas > > > > > > > > > > On Wed, Mar 20, 2013 at 2:10 PM, wzhao6898 at gmail.com < > wzhao6898 at gmail.com> > > wrote: > >> > >> Hi there, > >> > >> Maybe this has been discussed before, but where can I find the > >> proteomic package that was in version 1.8.2? > >> Thanks, > >> > >> DZ > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > > From andreas at sdsc.edu Thu Mar 21 12:03:50 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 21 Mar 2013 09:03:50 -0700 Subject: [Biojava-l] google summer of code project ideas Message-ID: Hi, The application deadline for organisations for this year's Google summer of code is coming up. So far we have four project proposals for BioJava, which is pretty good. All of them would be great contributions! http://biojava.org/wiki/Google_Summer_of_Code If anybody has additional suggestions or ideas, let's finalize this page by tomorrow, so Pjotr Prins, our GSoC admin for this year, can submit our application on time. (ultimate application deadline for organisations is the 29th) Thanks, Andreas From jjramirez at estudiantes.uci.cu Thu Mar 21 15:50:30 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Thu, 21 Mar 2013 15:50:30 -0400 (EDT) Subject: [Biojava-l] How to draw chromatograms ??? In-Reply-To: <7ee1c876-6b74-4385-928d-773c737cec97@ucimail4.uci.cu> Message-ID: <037b39bd-25d9-4e9e-b4cd-3ff2e064b631@ucimail4.uci.cu> Hello comunity I'm building an aplication for my thesis work. I have many ab1 and scf files and I need to draw the chromatograms. Biojava provides many classes to build and manage chromatograms, but how I can draw its ??? thanks for you time. Janier -- Universidad de las Ciencias Inform?ticas Janier http://www.uci.cu From andreas at sdsc.edu Sun Mar 24 12:37:50 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 24 Mar 2013 09:37:50 -0700 Subject: [Biojava-l] GSoC timeline Message-ID: Hi, The Open Bioinformatics Foundation just submitted our application for this year's Google Summer of Code. For a full timeline of the next couple of weeks see the bottom of this message. In the meanwhile we should still improve our project descriptions a bit: All possible Mentors (also people that are interested in being co-mentor but have not proposed a project) please update out GSoC page and add your name to the list of mentors. For the project descriptions, it would be good to improve the way the descriptions are structured. Can we add the following sections to each of the descriptions? Rationale, Approach & Goals, Difficulty and needed skills http://biojava.org/wiki/Google_Summer_of_Code Here the timeline for GSoC for the next couple of weeks. (taken from:) http://www.google-melange.com/gsoc/events/google/gsoc2013 April 1 - 5:Google program administrators review organization applications.April 8:19:00 UTCList of accepted mentoring organizations published on the *Google Summer of Code* 2013 site.April 9 - 21:Would-be student participants discuss application ideas with mentoring organizations.April 22:19:00 UTCStudent application period opens.May 3:19:00 UTCStudent application deadline.Interim Period:Mentoring organizations review and rank student proposals; where necessary, mentoring organizations may request further proposal detail from the student applicant.May 6: Mentoring organizations should have requested slots via their profile in Melange by this point. May 8:Slot allocations published to mentoring organizationsInterim Period:Slot allocation trades happen amongst organizations. Mentoring organizations review and rank student proposals; where necessary, mentoring organizations may request further proposal detail from the student applicant.May 22: First round of de-duplication checks happens; organizations work together to try to resolve as many duplicates as possible.May 24: 1. All mentors must be signed up and all student proposals matched with a mentor - 07:00 UTC 2. Student acceptance choice deadline. 3. IRC meeting to resolve any outstanding duplicate accepted students - 19:00 UTC #gsoc (organizations must send a delegate to represent them in this meeting regardless of if they are in a duplicate situation before the meeting.) May 27:19:00 UTCAccepted student proposals announced on the *Google Summer of Code* 2013 site. From jjramirez at estudiantes.uci.cu Mon Mar 25 10:00:38 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Mon, 25 Mar 2013 10:00:38 -0400 (EDT) Subject: [Biojava-l] Getting Phred Quality Scores In-Reply-To: <1c27b601-c0d6-47e1-b808-70657d34bab6@ucimail4.uci.cu> Message-ID: Hi Community ! I?m working with SCF and AB1 files and I need get the phred quality scores of each base. please, any suggestion or example ? Thanks ! -- There is no knowledge, that is not power http://www.uci.cu From sbliven at ucsd.edu Tue Mar 26 13:35:37 2013 From: sbliven at ucsd.edu (Spencer Bliven) Date: Tue, 26 Mar 2013 10:35:37 -0700 Subject: [Biojava-l] Biojava moving to Github Message-ID: Dear community, On the developer list we have been discussing moving the biojava code to github for some time. This transition is currently scheduled to occur this weekend. For users who get Biojava via binary jars or maven, this will have no effect on your projects. Users who compile the latest version of the source themselves may have to get a fresh version from github after April 1: biojava 3: https://github.com/biojava/biojava biojava 1: https://github.com/biojava/biojava-legacy I'll be working on improving documentation for the transition this week. For those interested in the migration process, see http://biojava.org/wiki/SVN_to_GIT_Migration. Some information about using git with eclipse is at http://biojava.org/wiki/BioJava3_eclipse#Anonymous_access_with_Git. And http://biojava.org/wiki/Get_source will soon be updated with the new instructions for getting the latest source code from git. Please let me know if anyone has suggestions or concerns. -Spencer From jeremy at lewi.us Wed Mar 27 08:50:52 2013 From: jeremy at lewi.us (Jeremy Lewi) Date: Wed, 27 Mar 2013 05:50:52 -0700 Subject: [Biojava-l] DNA: Many to one alignments Message-ID: HI biojava users, I'd like to align N DNA sequences to my reference sequence. I don't know which strand of my N query sequences will be the best match for my query sequence. Right, now I do this by doing 2N pairwise alignments where I separately align each query and its reverse complement to the reference. Is there an easier, more efficient way to do this and build the alignment profile for my N sequences to the reference? Thanks J From jjramirez at estudiantes.uci.cu Fri Mar 29 00:48:51 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Fri, 29 Mar 2013 00:48:51 -0400 (EDT) Subject: [Biojava-l] Phred Quality Scores and .qual format In-Reply-To: <7eed1cb2-7a8a-4d33-b57c-f1c252ed74d3@ucimail4.uci.cu> Message-ID: Hi guys ! I'm investigating for the whole genome assembly using AMOS Project. I need to obtain the Phred Quality Scores from Abi an Scf files, to then buil a .qual file, but my dude is obtaining the Scores, I have tried many time but I can't reach it !. Sorry for my English. Thanks for your time -- Universidad de las Ciencias Inform?ticas Janier J. Ram?rez Landaburo Facultad - 6 Tel-837-3121 http://www.uci.cu From biojava at hannes.oib.com Fri Mar 29 07:52:41 2013 From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=) Date: Fri, 29 Mar 2013 12:52:41 +0100 Subject: [Biojava-l] Phred Quality Scores and .qual format In-Reply-To: References: <7eed1cb2-7a8a-4d33-b57c-f1c252ed74d3@ucimail4.uci.cu> Message-ID: SCF can currently only be read in biojava-legacy. I am planning to port the code to BioJave 3 after the switch to git (i.e. next month) Until then, I think there are legacy-cookbook examples on how to read scf files. Hannes On Fri, Mar 29, 2013 at 5:48 AM, Janier J. Ram?rez < jjramirez at estudiantes.uci.cu> wrote: > Hi guys ! > > I'm investigating for the whole genome assembly using AMOS Project. > > I need to obtain the Phred Quality Scores from Abi an Scf files, to then > buil a .qual file, but my dude is obtaining the Scores, I have tried many > time but I can't reach it !. > > Sorry for my English. > > Thanks for your time > > > -- > > > Universidad de las Ciencias Inform?ticas > Janier J. Ram?rez Landaburo > Facultad - 6 > Tel-837-3121 > http://www.uci.cu > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From chapmanb at 50mail.com Fri Mar 1 02:39:11 2013 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu, 28 Feb 2013 21:39:11 -0500 Subject: [Biojava-l] 2013 BOSC/Broad Interoperability Hackathon + BOSC Codefest In-Reply-To: References: Message-ID: <87mwunsv1s.fsf@fastmail.fm> Michael; Thanks for publicizing these. I sent around a more general reminder about the events but definitely welcome Java folks to come out to the coding sessions (and BOSC itself). The hackathon at Broad will have a lot of programmers from the GenomeSpace team (http://www.genomespace.org/) so there will be plenty of Java object talk to go around, Brad > Just wanted to announce to and/or remind folks of two upcoming BOSC > and Biojava-related events: > > April 7-8, 2013: BOSC/Broad Interoperability Hackathon, Cambridge, MA > http://www.broadinstitute.org/events/interoperability-hackathon-2013/home > > July 17-18, 2013: Codefest 2013, Berlin > http://www.open-bio.org/wiki/Codefest_2013 > > michael > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From andreas at sdsc.edu Sun Mar 3 19:49:57 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 3 Mar 2013 11:49:57 -0800 Subject: [Biojava-l] GSoC 2013 is ON Message-ID: Hi, Pjotr Prins will be the GSoC project administrator for the Open Bioinformatics Foundation this year. I am passing along his message about this year's organisation and deadlines: Game on! GSoC 2013 is ON. I am running with the OBF project administration this year for the Google Summer of code (GSoC). First and foremost I want to thank Robert Buels and others for making OBF/GSoC a success in the previous three years! This year, Robert, Chris Fields and Hilmar Lapp will act as backup administrators. The deadline for the OBF application for GSoC2013 as a mentoring organisation is Friday March 29! See http://www.google-melange.com/gsoc/events/google/gsoc2013 Similar to previous years, each Bio* project needs to update and add project ideas on the project's individual OBF wiki page and create links from the main OBF page at http://www.open-bio.org/wiki/Google_Summer_of_Code (we will update the main information on that page soon). So, for each of the OBF projects that wants to do GSoC again this year: 1. Update the list of project ideas on your project's GSoC page (BioPython, BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done or no longer relevant, etc. For an example see http://bioruby.open-bio.org/wiki/Google_Summer_of_Code 2. Update the final list of project ideas on the main OBF GSoC page to match. http://www.open-bio.org/wiki/Google_Summer_of_Code 3. Register with gsoc at lists.open-bio.org 4. Announce it on that list when you are ready :) Anyone can submit a project idea! Former GSoC students are especially encouraged to contribute ideas to the mailing lists. Please have the updates done by Friday March 22nd. The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organisation again this year, so let's come up with some good ones! Pj. (Pjotr Prins) Important dates: * March 22nd: Finalise project ideas * March 29th: Deadline OBF mentoring organisation submission to Google http://www.open-bio.org/wiki/Google_Summer_of_Code From chrisrogersrogers at aol.com Wed Mar 13 18:35:28 2013 From: chrisrogersrogers at aol.com (chrisrogersrogers at aol.com) Date: Wed, 13 Mar 2013 14:35:28 -0400 (EDT) Subject: [Biojava-l] WORLDCOMP Strikes Again for the Last Time Message-ID: <8CFEE30AAB5884A-708-1310C@Webmail-d108.sysops.aol.com> I graduated from University of Florida (UFL) and am currently running a computer firm in Florida. I have attended WORLDCOMP http://www.world-academy-of-science.org in 2010. Except for few keynote speeches and presentations, the conference was very disappointing due to a large number of poor quality papers and cancellation of some sessions. I was instantly suspicious of this conference. Me and my UFL and UGA friends started a study on WORLDCOMP. We submitted a paper to WORLDCOMP 2011 and again (the same paper with a modified title) to WORLDCOMP 2012. This paper had numerous fundamental mistakes. Sample statements from that paper include: (1). Binary logic is fuzzy logic and vice versa (2). Pascal developed fuzzy logic (3). Object oriented languages do not exhibit any polymorphism or inheritance (4). TCP and IP are synonyms and are part of OSI model (5). Distributed systems deal with only one computer (6). Laptop is an example for a super computer (7). Operating system is an example for computer hardware Also, our paper did not express any conceptual meaning. However, it was accepted both the times without any modifications (and without any reviews) and we were invited to submit the final paper and a payment of $500+ fee to present the paper. We decided to use the fee for better purposes than making Prof. Hamid Arabnia (Chairman of WORLDCOMP) rich. After that, we received few reminders from WORLDCOMP to pay the fee but we never responded. We MUST say that you should look at the website http://sites.google.com/site/worlddump1 if you have any thoughts to submit a paper to WORLDCOMP. DBLP and other indexing agencies have stopped indexing WORLDCOMP?s proceedings since 2011 due to its fakeness. The status of your WORLDCOMP papers can be changed from ?scientific? to ?other? (i.e., junk or non-technical) at anytime. See the comments http://www.mail-archive.com/tccc at lists.cs.columbia.edu/msg05168.html of a respected researcher on this. Better not to have a paper than having it in WORLDCOMP and spoil the resume and peace of mind forever! Our study revealed that WORLDCOMP is a money making business, using UGA mask, for Prof. Hamid Arabnia. He is throwing out a small chunk of that money (around 20 dollars per paper published in WORLDCOMP?s proceedings) to his puppet who publicizes WORLDCOMP and also defends it at various forums, using fake/anonymous names. The puppet uses fake names and defames other conferences/people to divert traffic to WORLDCOMP. That is, the puppet does all his best to get a maximum number of papers published at WORLDCOMP to get more money into his (and Prof. Hamid Arabnia?s) pockets. Monte Carlo Resort (the venue of WORLDCOMP until 2012) has refused to provide the venue for WORLDCOMP?13 because of the fears of their image being tarnished due to WORLDCOMP?s fraudulent activities. WORLDCOMP will not be held after 2013. The paper submission deadline for WORLDCOMP?13 is March 18, 2013 (it will be extended many times, as usual) but still there are no committee members, no reviewers, and there is no conference Chairman. The only contact details available on WORLDCOMP?s website is just an email address! What bothers us the most is that Prof. Hamid Arabnia never posted an apology for the damage he has done to the research community. He is still trying to defend WORLDCOMP. Let us make a direct request to him: publish all reviews for all the papers (after blocking identifiable details) since 2000 conference. Reveal the names and affiliations of all the reviewers (for each year) and how many papers each reviewer had reviewed on average. We also request him to look at the Open Challenge at http://sites.google.com/site/dumpconf We think that it is our professional obligation to spread this message to alert the computer science community. Sorry for posting to multiple lists. Spreading the word is the only way to stop this bogus conference. Please forward this message to other mailing lists and people. We are shocked with Prof. Hamid Arabnia and his puppet?s activities http://worldcomp-fake-bogus.blogspot.com Search Google using the keywords ?worldcomp, fake? for additional links. Sincerely, Chris From jjramirez at estudiantes.uci.cu Tue Mar 19 15:52:33 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Tue, 19 Mar 2013 11:52:33 -0400 (EDT) Subject: [Biojava-l] Drawing chromatogram from ab1 file Message-ID: <7ee1c876-6b74-4385-928d-773c737cec97@ucimail4.uci.cu> Hello comunity I have some ab1 files and I need to draw the chromatogram usin biojava, already got the sequence, but now I need show the chromatogram. Somebody know the code to do this ? thanks for you time. Janier -- Universidad de las Ciencias Inform?ticas Janier J. Ram?rez Landaburo Facultad - 6 Tel-837-3121 From ngsbioinformatics at gmail.com Tue Mar 19 17:56:02 2013 From: ngsbioinformatics at gmail.com (Ryan Golhar) Date: Tue, 19 Mar 2013 13:56:02 -0400 Subject: [Biojava-l] Drawing chromatogram from ab1 file In-Reply-To: <7ee1c876-6b74-4385-928d-773c737cec97@ucimail4.uci.cu> References: <7ee1c876-6b74-4385-928d-773c737cec97@ucimail4.uci.cu> Message-ID: There are lots of programs available to do this. I have a Java program at http://github.com/golharam/ChromViewer that does this as well. On Tue, Mar 19, 2013 at 11:52 AM, Janier J. Ram?rez < jjramirez at estudiantes.uci.cu> wrote: > Hello comunity > > I have some ab1 files and I need to draw the chromatogram usin biojava, > already got the sequence, but now I need show the chromatogram. > Somebody know the code to do this ? > > thanks for you time. > > Janier > -- > > > Universidad de las Ciencias Inform?ticas > Janier J. Ram?rez Landaburo > Facultad - 6 > Tel-837-3121 > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From wzhao6898 at gmail.com Wed Mar 20 21:09:03 2013 From: wzhao6898 at gmail.com (wzhao6898 at gmail.com) Date: Wed, 20 Mar 2013 14:09:03 -0700 Subject: [Biojava-l] (no subject) Message-ID: Hi there, Maybe this has been discussed before, but where can I find the proteomic package that was in version 1.8.2? Thanks, DZ From wzhao6898 at gmail.com Wed Mar 20 21:10:03 2013 From: wzhao6898 at gmail.com (wzhao6898 at gmail.com) Date: Wed, 20 Mar 2013 14:10:03 -0700 Subject: [Biojava-l] Proteomic package in Biojava 3 Message-ID: Hi there, Maybe this has been discussed before, but where can I find the proteomic package that was in version 1.8.2? Thanks, DZ From andreas at sdsc.edu Wed Mar 20 22:33:23 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 20 Mar 2013 15:33:23 -0700 Subject: [Biojava-l] Proteomic package in Biojava 3 In-Reply-To: References: Message-ID: Hi, what functionality do you need exactly? There are several new modules in biojava 3 that contain related functionality. Probably the closest might be *biojava3-aa-prop *Physico chemial properties: http://biojava.org/wiki/BioJava:CookBook#Physico-Chemical_Properties_Computation Is this what you need? Andreas On Wed, Mar 20, 2013 at 2:10 PM, wzhao6898 at gmail.com wrote: > Hi there, > > Maybe this has been discussed before, but where can I find the > proteomic package that was in version 1.8.2? > Thanks, > > DZ > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From andreas at sdsc.edu Wed Mar 20 22:46:46 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 20 Mar 2013 15:46:46 -0700 Subject: [Biojava-l] Proteomic package in Biojava 3 In-Reply-To: References: Message-ID: I think Digest and related classes have not been migrated to biojava 3 as of yet. However that code for digesting sequences seems quite independent and should be easy to migrate that over to biojava 3.... Andreas On Wed, Mar 20, 2013 at 3:40 PM, wzhao6898 at gmail.com wrote: > Thanks for the reply, I'm actually interested in the Digest and related > classes. > > DZ > > On Wed, Mar 20, 2013 at 3:33 PM, Andreas Prlic wrote: > > Hi, > > > > what functionality do you need exactly? There are several new modules in > > biojava 3 that contain related functionality. Probably the closest might > be > > > > biojava3-aa-prop Physico chemial properties: > > > > > http://biojava.org/wiki/BioJava:CookBook#Physico-Chemical_Properties_Computation > > > > Is this what you need? > > > > Andreas > > > > > > > > > > On Wed, Mar 20, 2013 at 2:10 PM, wzhao6898 at gmail.com < > wzhao6898 at gmail.com> > > wrote: > >> > >> Hi there, > >> > >> Maybe this has been discussed before, but where can I find the > >> proteomic package that was in version 1.8.2? > >> Thanks, > >> > >> DZ > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > > From andreas at sdsc.edu Thu Mar 21 16:03:50 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 21 Mar 2013 09:03:50 -0700 Subject: [Biojava-l] google summer of code project ideas Message-ID: Hi, The application deadline for organisations for this year's Google summer of code is coming up. So far we have four project proposals for BioJava, which is pretty good. All of them would be great contributions! http://biojava.org/wiki/Google_Summer_of_Code If anybody has additional suggestions or ideas, let's finalize this page by tomorrow, so Pjotr Prins, our GSoC admin for this year, can submit our application on time. (ultimate application deadline for organisations is the 29th) Thanks, Andreas From jjramirez at estudiantes.uci.cu Thu Mar 21 19:50:30 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Thu, 21 Mar 2013 15:50:30 -0400 (EDT) Subject: [Biojava-l] How to draw chromatograms ??? In-Reply-To: <7ee1c876-6b74-4385-928d-773c737cec97@ucimail4.uci.cu> Message-ID: <037b39bd-25d9-4e9e-b4cd-3ff2e064b631@ucimail4.uci.cu> Hello comunity I'm building an aplication for my thesis work. I have many ab1 and scf files and I need to draw the chromatograms. Biojava provides many classes to build and manage chromatograms, but how I can draw its ??? thanks for you time. Janier -- Universidad de las Ciencias Inform?ticas Janier http://www.uci.cu From andreas at sdsc.edu Sun Mar 24 16:37:50 2013 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 24 Mar 2013 09:37:50 -0700 Subject: [Biojava-l] GSoC timeline Message-ID: Hi, The Open Bioinformatics Foundation just submitted our application for this year's Google Summer of Code. For a full timeline of the next couple of weeks see the bottom of this message. In the meanwhile we should still improve our project descriptions a bit: All possible Mentors (also people that are interested in being co-mentor but have not proposed a project) please update out GSoC page and add your name to the list of mentors. For the project descriptions, it would be good to improve the way the descriptions are structured. Can we add the following sections to each of the descriptions? Rationale, Approach & Goals, Difficulty and needed skills http://biojava.org/wiki/Google_Summer_of_Code Here the timeline for GSoC for the next couple of weeks. (taken from:) http://www.google-melange.com/gsoc/events/google/gsoc2013 April 1 - 5:Google program administrators review organization applications.April 8:19:00 UTCList of accepted mentoring organizations published on the *Google Summer of Code* 2013 site.April 9 - 21:Would-be student participants discuss application ideas with mentoring organizations.April 22:19:00 UTCStudent application period opens.May 3:19:00 UTCStudent application deadline.Interim Period:Mentoring organizations review and rank student proposals; where necessary, mentoring organizations may request further proposal detail from the student applicant.May 6: Mentoring organizations should have requested slots via their profile in Melange by this point. May 8:Slot allocations published to mentoring organizationsInterim Period:Slot allocation trades happen amongst organizations. Mentoring organizations review and rank student proposals; where necessary, mentoring organizations may request further proposal detail from the student applicant.May 22: First round of de-duplication checks happens; organizations work together to try to resolve as many duplicates as possible.May 24: 1. All mentors must be signed up and all student proposals matched with a mentor - 07:00 UTC 2. Student acceptance choice deadline. 3. IRC meeting to resolve any outstanding duplicate accepted students - 19:00 UTC #gsoc (organizations must send a delegate to represent them in this meeting regardless of if they are in a duplicate situation before the meeting.) May 27:19:00 UTCAccepted student proposals announced on the *Google Summer of Code* 2013 site. From jjramirez at estudiantes.uci.cu Mon Mar 25 14:00:38 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Mon, 25 Mar 2013 10:00:38 -0400 (EDT) Subject: [Biojava-l] Getting Phred Quality Scores In-Reply-To: <1c27b601-c0d6-47e1-b808-70657d34bab6@ucimail4.uci.cu> Message-ID: Hi Community ! I?m working with SCF and AB1 files and I need get the phred quality scores of each base. please, any suggestion or example ? Thanks ! -- There is no knowledge, that is not power http://www.uci.cu From sbliven at ucsd.edu Tue Mar 26 17:35:37 2013 From: sbliven at ucsd.edu (Spencer Bliven) Date: Tue, 26 Mar 2013 10:35:37 -0700 Subject: [Biojava-l] Biojava moving to Github Message-ID: Dear community, On the developer list we have been discussing moving the biojava code to github for some time. This transition is currently scheduled to occur this weekend. For users who get Biojava via binary jars or maven, this will have no effect on your projects. Users who compile the latest version of the source themselves may have to get a fresh version from github after April 1: biojava 3: https://github.com/biojava/biojava biojava 1: https://github.com/biojava/biojava-legacy I'll be working on improving documentation for the transition this week. For those interested in the migration process, see http://biojava.org/wiki/SVN_to_GIT_Migration. Some information about using git with eclipse is at http://biojava.org/wiki/BioJava3_eclipse#Anonymous_access_with_Git. And http://biojava.org/wiki/Get_source will soon be updated with the new instructions for getting the latest source code from git. Please let me know if anyone has suggestions or concerns. -Spencer From jeremy at lewi.us Wed Mar 27 12:50:52 2013 From: jeremy at lewi.us (Jeremy Lewi) Date: Wed, 27 Mar 2013 05:50:52 -0700 Subject: [Biojava-l] DNA: Many to one alignments Message-ID: HI biojava users, I'd like to align N DNA sequences to my reference sequence. I don't know which strand of my N query sequences will be the best match for my query sequence. Right, now I do this by doing 2N pairwise alignments where I separately align each query and its reverse complement to the reference. Is there an easier, more efficient way to do this and build the alignment profile for my N sequences to the reference? Thanks J From jjramirez at estudiantes.uci.cu Fri Mar 29 04:48:51 2013 From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=) Date: Fri, 29 Mar 2013 00:48:51 -0400 (EDT) Subject: [Biojava-l] Phred Quality Scores and .qual format In-Reply-To: <7eed1cb2-7a8a-4d33-b57c-f1c252ed74d3@ucimail4.uci.cu> Message-ID: Hi guys ! I'm investigating for the whole genome assembly using AMOS Project. I need to obtain the Phred Quality Scores from Abi an Scf files, to then buil a .qual file, but my dude is obtaining the Scores, I have tried many time but I can't reach it !. Sorry for my English. Thanks for your time -- Universidad de las Ciencias Inform?ticas Janier J. Ram?rez Landaburo Facultad - 6 Tel-837-3121 http://www.uci.cu From biojava at hannes.oib.com Fri Mar 29 11:52:41 2013 From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=) Date: Fri, 29 Mar 2013 12:52:41 +0100 Subject: [Biojava-l] Phred Quality Scores and .qual format In-Reply-To: References: <7eed1cb2-7a8a-4d33-b57c-f1c252ed74d3@ucimail4.uci.cu> Message-ID: SCF can currently only be read in biojava-legacy. I am planning to port the code to BioJave 3 after the switch to git (i.e. next month) Until then, I think there are legacy-cookbook examples on how to read scf files. Hannes On Fri, Mar 29, 2013 at 5:48 AM, Janier J. Ram?rez < jjramirez at estudiantes.uci.cu> wrote: > Hi guys ! > > I'm investigating for the whole genome assembly using AMOS Project. > > I need to obtain the Phred Quality Scores from Abi an Scf files, to then > buil a .qual file, but my dude is obtaining the Scores, I have tried many > time but I can't reach it !. > > Sorry for my English. > > Thanks for your time > > > -- > > > Universidad de las Ciencias Inform?ticas > Janier J. Ram?rez Landaburo > Facultad - 6 > Tel-837-3121 > http://www.uci.cu > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l >