From lijo.skb at gmail.com Tue May 5 03:56:35 2009 From: lijo.skb at gmail.com (Lijo) Date: Tue, 5 May 2009 13:26:35 +0530 Subject: [BiO BB] protein-protein interaction prediction In-Reply-To: References: Message-ID: Dear Kie, some of my lab colleges have been developed a computing method to predict Hubness of proteins out of their amino sequences. they used diversity index static to develope the method. they have got interesting result with publishable Sn, Sp and accuracy. they can share the method if you are interested. best, Lijo Anto M.A, Centre for Bioinformatics Universityof Kerala. On Wed, Apr 29, 2009 at 9:46 PM, Kie Kyon Huang wrote: > Hi, > > Is there any good software to predict protein-protein interaction at genome > level? > > I prefer methods that do not need to incorporate orthology so that the > network could be expanded to more gene. > > Thanks a lot > > Kie Kyon > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Centre for Bioinformatics, University of Kerala, India. +91 9446515705(res) From gorrieri at cs.unibo.it Tue May 5 05:05:55 2009 From: gorrieri at cs.unibo.it (Roberto Gorrieri) Date: Tue, 5 May 2009 11:05:55 +0200 Subject: [BiO BB] Computational Methods in Systems Biology (CMSB'09) - call for posters Message-ID: *************************************************************** Due to many requests, we have been able to accomodate a poster session at the 7th International Conference on COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY (CMSB 2009) August 31 -- September 1, 2009 Bologna, Italy http://cmsb09.cs.unibo.it/ *************************************************************** Important Dates --------------- May, 30: Submission of posters June, 15: Notification of acceptance/rejection August 31 -- September 1: Conference Submissions, at most two pages long, describing the topic and main points to be presented in the poster, should be submitted electronically as PDF via Easychair at * http://www.easychair.org/conferences/?conf=cmsb09 *************************************************************** From mourad12345678 at yahoo.com Tue May 5 21:12:01 2009 From: mourad12345678 at yahoo.com (Mourad Elloumi) Date: Tue, 5 May 2009 18:12:01 -0700 (PDT) Subject: [BiO BB] Motif-Finding Problems Complexities Message-ID: <875034.65090.qm@web31505.mail.mud.yahoo.com> Dear All, We are seeking the complexities of the following Motif-Finding Problems : 1. Planted (l,d)-Motif Problem (PMP) 2. Extended (l,d)-Motif Problem (ExMP) 3. Further Extended (l,d)-Motif Problem (FExMP) 4. Edited Motif Search Problem (EdMP) 5. Simple Motifs Search Problem (SMS) Do you know have any references on these complexities? Thanks. Best regards, Mourad. ______________________________________________________ E.Mail:Mourad.Elloumi at fsegt.rnu.tn URL :www.esstt.rnu.tn/utic/english/memb_elloumi.html ______________________________________________________ From dan.bolser at gmail.com Wed May 6 03:56:58 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 6 May 2009 08:56:58 +0100 Subject: [BiO BB] Motif-Finding Problems Complexities In-Reply-To: <875034.65090.qm@web31505.mail.mud.yahoo.com> References: <875034.65090.qm@web31505.mail.mud.yahoo.com> Message-ID: <2c8757af0905060056q23ab1a16r8c7a040d5ae7627c@mail.gmail.com> 2009/5/6 Mourad Elloumi : > > Dear All, > > We are seeking the complexities of the following Motif-Finding Problems : > > ?1. Planted (l,d)-Motif Problem (PMP) > ?2. Extended (l,d)-Motif Problem (ExMP) > ?3. Further Extended (l,d)-Motif Problem (FExMP) > ?4. Edited Motif Search Problem (EdMP) > ?5. Simple Motifs Search Problem (SMS) > > Do you know have any references on these complexities? Thanks. Hi Mourad, Do you have some references describing these Motif-Finding Problems in more detail? Cheers, Dan. > Best regards, > Mourad. > ______________________________________________________ > > E.Mail:Mourad.Elloumi at fsegt.rnu.tn > URL ? :www.esstt.rnu.tn/utic/english/memb_elloumi.html > ______________________________________________________ > > > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From EliDraizen at drewschool.org Thu May 7 19:06:29 2009 From: EliDraizen at drewschool.org (Eli Draizen) Date: Thu, 7 May 2009 16:06:29 -0700 Subject: [BiO BB] college In-Reply-To: References: <9BE4A105CF42C64A844E8077087BC21901E88141@mercury.drewschool.org> Message-ID: <9BE4A105CF42C64A844E8077087BC21901E88144@mercury.drewschool.org> Hello- Thanks for taking the time to write me back. Everyone seems to have a different opinion on this. One of my top schools is UC Santa Cruz and the professor there differed from your opinions. He said to major in bioinformatics from the start. But as Keith said, I might spread myself too thin if I do that. I think I should visit so I can see how the program is. Thanks, Eli Draizen _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From marchywka at hotmail.com Sat May 9 17:08:48 2009 From: marchywka at hotmail.com (Mike Marchywka) Date: Sat, 9 May 2009 17:08:48 -0400 Subject: [BiO BB] college In-Reply-To: <9BE4A105CF42C64A844E8077087BC21901E88144@mercury.drewschool.org> References: <9BE4A105CF42C64A844E8077087BC21901E88141@mercury.drewschool.org> <9BE4A105CF42C64A844E8077087BC21901E88144@mercury.drewschool.org> Message-ID: > Date: Thu, 7 May 2009 16:06:29 -0700 > From: drewschool.org > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] college > > Hello- > Thanks for taking the time to write me back. Everyone seems to have a > different opinion on this. One of my top schools is UC Santa Cruz and > the professor there differed from your opinions. He said to major in > bioinformatics from the start. But as Keith said, I might spread myself > too thin if I do that. I think I should visit so I can see how the > program is. I didn't respond earlier but after looking at the Drew site, it seems to have a liberal arts focus as there didn't appear to be any technical projects listed. Without remembering exactly what you were asking, you may want to consider a Chemical Engineering program. You probably want to develop portable problem analysis skills and have basic knowledge in many fields so you can read the literature in those fields and become useful as needed. If you can predict the future or hope to author a new field ( optimistic but not impossible) you can specialize in the relevant areas from the beginning. Chemical Engineering may make some sense but even in Electrical Engineering (my field) you can get appreciable chemistry and physics background along with things like optics or other technical fields. Computers are an obvious thing with EE but it can be much broader than that. Check out some engineering curricula they should be online. You can probably even contact nearby authors and see if they can make a few comments back to you or you can visit ( obviously you can email people anywhere if you know what you are looking for ), http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=San+Francisco+bioinformatics If you go get cygwin or some non-windoze stuff you can play around with a lot yourself right now. I also advocate this approach for much younger kids ( I started with computers and a chemistry set in junior high and still find the experience useful- I wish I had source code from an old Z80 computer to use on a cell phone today LOL ). Find something you like and remember that this is more than clean, tractable computer stuff done in software- the real underlying phenomena can be messy and confusing and the computer stuff is just an abstraction you need to relate back to something relevant. With polymers- from plastics to proteins to genes- informatics can be pretty good but even there you have things that the computer currently misses. > > Thanks, > Eli Draizen _________________________________________________________________ Windows Live?: Keep your life in sync. http://windowslive.com/explore?ocid=TXT_TAGLM_BR_life_in_synch_052009 From ykalidas at gmail.com Tue May 12 00:52:23 2009 From: ykalidas at gmail.com (Kalidas Yeturu) Date: Tue, 12 May 2009 10:22:23 +0530 Subject: [BiO BB] Program for superposition of 3D point sets Message-ID: <5632703b0905112152v7525cba0y7940e2d2f536d4fc@mail.gmail.com> Dear All I would greatly appreciate if you can give a program that optimally superposes a pair of point sets (3D) and outputs rotation and translation matrices corresponding to each solution. I searched to my best in the web but could not find one. Please do NOT point to - Protein-Protein superposition web-servers/standalone ones - Programs that require residues to be contiguous in order to superpose - Motif search programs - IEEE/other literature on point set superposition algorithms without corresponding implementation I need preferably C/Fortran program or as a last choice a library function that I can call from other C programs. Thanking You -- With Regards Kalidas Y http://ssl.serc.iisc.ernet.in/~kalidas From tcan at ceng.metu.edu.tr Thu May 14 17:34:02 2009 From: tcan at ceng.metu.edu.tr (Tolga Can) Date: Fri, 15 May 2009 00:34:02 +0300 Subject: [BiO BB] Program for superposition of 3D point sets In-Reply-To: <5632703b0905112152v7525cba0y7940e2d2f536d4fc@mail.gmail.com> References: <5632703b0905112152v7525cba0y7940e2d2f536d4fc@mail.gmail.com> Message-ID: <8ad607cb0905141434j419bcd8cnfd1035c62fd15059@mail.gmail.com> Dear Kalidas, I have a program written in Java that superposes a pair of point sets in 3D. It is an implementation of Umeyama's algorithm. It can easily be converted to C, however it computes the singular value decomposition of a three by three matrix using an external library (Jama). But I'm sure you can find SVD implementations in C and integrate into your code. The zip bundle at the url below includes the Jama library. Just write "java superimpose" to run the program. http://www.ceng.metu.edu.tr/~tcan/misc/superimpose.zip Hope this helps. Tolga Can On Tue, May 12, 2009 at 7:52 AM, Kalidas Yeturu wrote: > Dear All > > I would greatly appreciate if you can give a program that optimally > superposes a pair of point sets (3D) and outputs rotation and translation > matrices corresponding to each solution. > > I searched to my best in the web but could not find one. > > Please do NOT point to > - Protein-Protein superposition web-servers/standalone ones > - Programs that require residues to be contiguous in order to superpose > - Motif search programs > - IEEE/other literature on point set superposition algorithms without > corresponding implementation > > I need preferably C/Fortran program or as a last choice a library function > that I can call from other C programs. > > Thanking You > > -- > With Regards > Kalidas Y > http://ssl.serc.iisc.ernet.in/~kalidas > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From marchywka at hotmail.com Mon May 18 09:48:04 2009 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 18 May 2009 09:48:04 -0400 Subject: [BiO BB] high school [ was college ] In-Reply-To: <9BE4A105CF42C64A844E8077087BC21901E88144@mercury.drewschool.org> References: <9BE4A105CF42C64A844E8077087BC21901E88141@mercury.drewschool.org> <9BE4A105CF42C64A844E8077087BC21901E88144@mercury.drewschool.org> Message-ID: You may be interested in this PR on a science fair result and see if it gives you any thoughts on what kinds of programs you may like to pursue. The specific topics may or may not be of interest but you can get some idea of what is interesting or find places to look for more details, http://www.nih.gov/news/health/may2009/nida-15a.htm To your point, The Impact of Third Hand Smoke on Risk for Genetic Mutations Wins First Place Addiction Science Award at 2009 Intel ISEF Competition Forensic and Computer Science Projects Also Impress NIDA The third place Addiction Science Award was given to a computer science project, "Complex Evaluation of Danger and Tranquility in Urban Settings: An Immunocomputing Intelligence Approach," developed by 18-year-old Lucia Mocz, a senior at Mililani High School in Mililani, Hawaii. Using an artificial intelligence algorithm, Mocz was able to generate highly detailed maps that integrate correlated indicators of danger and tranquility in the urban region of her home town. Note that the top winners were high school kids playing with flies and tobacco and considering if carnivores will avoid corpses of human drug users- science is not always about people in white coats with expensive equipment doing obscure experiments all the time. You are looking for relevant questions to answer and finding approaches that give you as much information as possible with as little cost and effort or ambiguity. It gets even more mundane than that especially with emerging diseases and household ecology ( those pink stains near home water fixtures should make you think about bioinformatics...). ---------------------------------------- > From: > To: bbb at bioinformatics.org > Subject: RE: [BiO BB] college > Date: Sat, 9 May 2009 17:08:48 -0400 > > > >> Date: Thu, 7 May 2009 16:06:29 -0700 >> From: drewschool.org >> To: bbb at bioinformatics.org >> Subject: Re: [BiO BB] college >> >> Hello- >> Thanks for taking the time to write me back. Everyone seems to have a >> different opinion on this. One of my top schools is UC Santa Cruz and >> the professor there differed from your opinions. He said to major in >> bioinformatics from the start. But as Keith said, I might spread myself >> too thin if I do that. I think I should visit so I can see how the >> program is. > > I didn't respond earlier but after looking at the Drew site, it > seems to have a liberal arts focus as there didn't appear to be > any technical projects listed. Without > remembering exactly what you were asking, you may want to consider _________________________________________________________________ Hotmail? goes with you. http://windowslive.com/Tutorial/Hotmail/Mobile?ocid=TXT_TAGLM_WL_HM_Tutorial_Mobile1_052009 From paolo.romano at istge.it Wed May 27 12:19:51 2009 From: paolo.romano at istge.it (Paolo Romano) Date: Wed, 27 May 2009 18:19:51 +0200 Subject: [BiO BB] NETTAB 2009: Last Call for Participation Message-ID: <200905271634.n4RGYosu014008@ibm43p.biotech.ist.unige.it> Last Call for Participation NETTAB 2009 Workshop on "Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development" with a Special Session on: "Methods and Tools for RNA Structure and Functional Analysis" June 10-13, 2009 Department of Computer Science, University of Catania, Italy http://www.nettab.org/2009/ KEYNOTE TALKS RNA WikiProject: Community annotation of RNA families Alex Bateman, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK. Who are you? Managing collaborative digital identities in bioinformatics with myExperiment Duncan Hull, School of Chemistry, University of Manchester, Manchester, UK. Semantically Integrated eCommunities in Biomedicine: Next-Generation Models of Biomedical Communication Tim Clark, Director of Informatics, MassGeneral Institute for Neurodegenerative Disease Neurology Research Department, Massachusetts General Hospital, Boston, USA. Bacterial Phylogeny and Taxonomy in the High-Throughput Sequencing World Gabriel Valiente, Technical University of Catalonia, Department of Software, Barcelona, Spain. Non coding RNAs (title to be confirmed) Doron Betel, MSKCC - Computational Biology Center, New York, USA . SELECTED ORAL COMMUNICATIONS The DC-THERA Directory: A Knowledge Management System to Support Collaboration on Dendritic Cell and Immunology Research Michaela Guendel, Ciro Scognamiglio, Marco Brandizi and Andrea Splendiani Bioinformatics Experimentation in a New Agent-Based Infrastructure OpenKnowledge Dietlind Gerloff, Xueping Quan, Adrian de Pinninck, Paolo Besana, Siu-wai Leung, Marco Schorlemmer and David Robertson Abstraction based cooperation for the design of bioinformatics workflows Fr?d?ric Cadier and Philippe Picouet Biomedical applications in the EELA-2 Project Leandro N Ciuffo and Rafael Mayo Make Histri: collaborative curation of exchange histories of bacterial and archaeal type strains Bert Verslyppe, Paul De Vos, Bernard De Baets and Peter Dawyndt SBMM Assistant: Social Pathway Annotation Ismael Navas-Delgado, Alejandro del Real-Chicharro, Francisca S?nchez-Jim?nez and Jose F Aldana Montes GePh-CARD: an information exchange application for an Hub & Spoke Network for Skeletal Dysplasias Marina Mordenti and Luca Sangiorgi ProDaMa-C: a collaborative web application to generate specialized protein structure datasets Giuliano Armano and Andrea Manconi RNA tertiary structure prediction with ModeRNA Magdalena Musielak, Kristian Rother, Tomasz Puton and Janusz M. Bujnicki Improved heuristic for pairwise RNA secondary structure prediction Olivier Perriquet and Pedro Barahona Analysing the microRNA-17-92/Myc/E2F/RB Compound Toggle Switch by Theorem Proving Giampaolo Bella and Pietro Li? Mapping miRNA genes on human fragile sites and translocation breakpoints Alfredo Ferro, rosalba giugno, Alessandro Lagan?, Alfredo Pulvirenti and Francesco Russo MicroRNA.gr: A suite of web based tools for elucidating microRNA function Giorgio L. Papadopoulos, Panagiotis Alexiou, Manolis Maragkakis, Martin Reczko and Artemis G. Hatzigeorgiou miRScape: A Cytoscape Plugin to Annotate Biological Networks with microRNAs Alfredo Ferro, rosalba giugno, Alessandro Lagan?, Misael Mongiov?, Giuseppe Pigola, Alfredo Pulvirenti, Gary Bader and Dennis Shasha POSTERS A web site supporting collaborative activities within the Italian Network for Oncology Bioinformatics Silvia Giuliani, Elda Rossi, Stefania Parodi and Paolo Romano Prediction of human targets for viral encoded microRNAs Alessandro Lagan?, Stefano Forte, Rosalba Giugno, Alfredo Pulvirenti and Alfredo Ferro Genome-wide microRNA target gene identification and annotation using multiple prediction algorithms Dario Corrada, Luciano Milanesi and Daniele Catalucci Design of highly specific synthetic miRNAs Alessandro Lagan?, Stefano Forte, Angela Papa, Rosalba Giugno, Alfredo Pulvirenti, Dennis Shasha and Alfredo Ferro NETTAB '09 - Ninth International Workshop on Network Tools and Applications in Biology 10-13 June 2009, Catania, Italy http://www.nettab.org/2009/ Paolo Romano (paolo.romano at istge.it) Bioinformatics National Cancer Research Institute (IST)