From hlapp at gmx.net Wed Mar 3 11:23:41 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 3 Mar 2010 11:23:41 -0500 Subject: [BiO BB] Call for Abstracts open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) Message-ID: <86785C02-A2F8-4154-B289-A16A0CA123D2@gmx.net> The Call for Abstracts for full talks is now open for the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs/index.php/ievobio/ 2010. See below for instructions. Accepted talks will be about 15-20 minutes in length and will be presented during the full talk sessions in the morning of each of the two conference days, following the day's keynote presentation. Submitted talks should be in the area of informatics aimed at advancing research in phylogenetics, evolution, and biodiversity, including new tools, cyberinfrastructure development, large-scale data analysis, and visualization. Submissions consist of a title and an abstract at most 1 page long. The abstract should provide an overview of the talk's subject. As the number of program slots for full talks is limited, the abstract should give enough detail so reviewers can decide whether the submission merits a full talk or whether it should be moved to one of the lightning talk sessions. If the subject of the talk is a specific software for use by the research community, the abstract must state the license and give the URL where the source code is available so reviewers can verify that the open-source requirement(*) is met. The deadline for submission is April 8, 2010. We intend to notify authors of accepted talks before early registration for iEvoBio (and Evolution) ends. Further instructions for submission are at the following URL: http://ievobio.org/ocs/index.php/ievobio/2010/information/presenters Full talks are 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Lightning talks (5 mins long), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of- a-Feather gatherings. The Call for Challenge entries is already open (see http://ievobio.org/challenge.html), and information on how to contribute to the other 3 sessions is forthcoming. More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2010 Organizing Committee: Rod Page (University of Glasgow) Cecile Ane (University of Wisconsin at Madison) Rob Guralnick (University of Colorado at Boulder) Hilmar Lapp (NESCent) Cynthia Parr (Encyclopedia of Life) Michael Sanderson (University of Arizona) (*) iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software development (see http://www.opensource.org/docs/definition.php) and reuse within the research community. For this reason, if a submitted talk concerns a specific software system for use by the research community, that software must be licensed with a recognized Open Source License (see http://www.opensource.org/licenses/), and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs, Subversion, git, Bazaar, or Mercurial. Authors of full talks who cannot meet this requirement at the time of submission should state their intentions, and are advised that the requirement must be met by June 27 at the latest. From Albert.Lai at osumc.edu Thu Mar 4 13:41:29 2010 From: Albert.Lai at osumc.edu (Lai, Albert) Date: Thu, 4 Mar 2010 13:41:29 -0500 Subject: [BiO BB] Call for Papers/Demos: 1st ACM International Conference on Health Informatics (IHI) Message-ID: <19AF8C50-DA28-4BE4-BB0B-45AE59587941@osumc.edu> CALL FOR PAPERS, Association for Computing Machinery (ACM) 1st ACM International Conference on Health Informatics (IHI) IHI 2010 November 11-12, 2010 Washington, DC http://ihi2010.sighi.org SCOPE OF THE CONFERENCE We cordially invite you to submit your contribution to the 2010 ACM International Conference on Health Informatics (IHI 2010). IHI 2010 is ACM's premier community forum concerned with the application of computer and information science principles and information and communication technology to problems in healthcare, public health, the delivery of healthcare services and consumer health as well as the related social and ethical issues. For technical contributions, IHI 2010 is primarily interested in end-to-end applications, systems, and technologies, even if available only in prototype form. Therefore, we strongly encourage authors to submit their original contributions describing their algorithmic and methodological contributions providing an application-oriented context. For social/behavioral scientific contributions, we are interested in empirical studies of health-related information needs, seeking, sharing and use, as well as socio-technical studies of heath information technology implementation and use. Topics of interest for this conference cover various aspects of health informatics, including but not limited to the following: - Accessibility and Web-enabled technologies - Analytics applied to direct and remote clinical care - Assistive and adaptive ubiquitous computing technologies - Biosurveillance - Brain computer interface - Cleaning, preprocessing, and ensuring quality and integrity of medical records - Computational support for patient-centered and evidence-based care - Consumer health and wellness informatics applications - Consumer and clinician health information needs, seeking, sharing and use - Continuous monitoring and streaming technologies - Data management, privacy, security, and confidentiality - Display and visualization of medical data - E-communities and networks for patients and consumers - E-healthcare infrastructure design - E-learning for spreading health informatics awareness - Engineering of medical data - Health information system framework and enterprise architecture in the developing world - Human-centered design of health informatics systems - Information retrieval for health applications - Information technologies for the management of patient safety and clinical outcomes - Innovative applications in electronic health records (e.g., ontology or semantic technology, using continuous biomedical signals to trigger alerts) - Intelligent medical devices and sensors - Issues involving interoperability and data representation in healthcare delivery - Keyword and multifaceted search over structured electronic health records - Knowledge discovery for improving patient-provider communication - Large-scale longitudinal mining of medical records - Medical compliance automation for patients and institutions - Medical recommender system (e.g., medical products, fitness programs) - Multimodal medical signal analysis - Natural language processing for biomedical literature, clinical notes, and health consumer texts - Novel health information systems for chronic disease management - Optimization models for planning and recommending therapies - Personalized predictive modeling for clinical management (e.g., trauma, diabetes mellitus, sleep disorders, substance abuse) - Physiological modeling - Semantic Web, linked data, ontology, and healthcare - Sensor networks and systems for pervasive healthcare - Social studies of health information technologies - Survival analysis and related methods for estimating hazard functions - System software for complex clinical studies that involve combinations of clinical, genetic, genomic, imaging, and pathology data - Systems for cognitive and decision support - Technologies for capturing and documenting clinical encounter information in electronic systems - User-interface design issues applied to medical devices and systems Each contribution will be carefully evaluated by a set of reviewers, including experts with multidisciplinary experience spanning computing, information science, social and behavioral sciences, public health, medicine, and nursing as appropriate, to ensure that proper and comprehensive peer-review analysis and feedback can be provided to authors. Submissions will be judged on validity, originality, technical strength, practical and clinical significance, quality of presentation, and relevance to the conference topics. Because of IHI's multidisciplinary nature, the review process will include at least a computing expert and a health expert as well as a review editor to reconcile the evaluation, making a single recommendation to the Program Committee Co-Chairs. This process is designed to ensure that experts from multiple areas can assess the importance and validity of the work. Therefore, we encourage coherent, application-driven submissions where in-depth ideas from a variety of fields are presented about important problems in health informatics. The conference will accept both regular and short papers. Regular papers (6-10 pages in length) will describe more mature ideas, where a substantial amount of implementation, experimentation, or data collection and analysis will be described. Short papers (1-5 pages) can be less formal and will describe innovative ideas where minimal validation and implementation have occurred and can be described. All papers will appear in the ACM Digital Library. The best papers of IHI 2010 will be considered for a special issue of Springer's Journal of Medical Systems. Submitted papers must not have appeared in, or be under consideration for, another conference, workshop, journal, or other target of publication. All aspects of the submission and notification process will be handled electronically. Submissions must adhere to the following formatting instructions: " Papers must adhere to the ACM Proceedings Format available for LaTex, WordPerfect, WordPerfect 9, and Word. Changing the template's font size, margins, inter-column spacing, or line spacing is prohibited. Each paper must be submitted as a single PDF file, formatted for 8.5" x 11" paper. " The length of submission depends on the type of submission: - Regular papers must be 6-10 pages long. - Short papers may be at most 5 pages long. " Each paper must provide an appendix (which is excluded from the page limit) indicating the preferred review approach, including: - The preferred allocation of reviewing expertise. This can be done by electing the primary and secondary focus of the paper (e.g., Computing, Information Science, Medicine, Nursing, and Social/Behavioral Science). - A bulleted list with up to 3 topics covered in the paper (from the list of conference topics presented above) IMPORTANT DATES Abstract submission deadline: June 2, 2010 11:30pm EST Paper submission deadline: June 4, 2010 11:30pm EST Notification of acceptance: August 6, 2010 11:30pm EST Camera-ready copy due: August 16, 2010 11:30pm EST General Chair ?mit ?ataly?rek, Ohio State University (catalyurek.1 at osu dot edu) Honorary General Chair Gang Luo, IBM Research (luog at us dot ibm dot com) Program Committee Co-Chairs Henrique Andrade, IBM Research (hcma at us dot ibm dot com) Neil R. Smalheiser, University of Illinois - Chicago (neils at uic dot edu) Steering Committee Members Dorin Comaniciu, Siemens Corporate Research Michael D. Larsen, George Washington University Ching-Yung Lin, IBM Research Chunqiang Tang, IBM Research YingLi Tian, City College of New York Olivier Verscheure, IBM Research Michael Weiner, Indiana University Honorary Steering Committee members Marion J. Ball, Johns Hopkins University & IBM Research Joseph A. Konstan, University of Minnesota Blackford Middleton, Partners Healthcare System & Harvard Medical School Joel H. Saltz, Emory University PROGRAM COMMITTEE MEMBERS To be finalized _________________________________________________________ CALL FOR DEMOS 1st ACM International Conference on Health Informatics (IHI 2010) IHI 2010 November 11-12, 2010 Washington, DC http://ihi2010.sighi.org SCOPE OF THE DEMO TRACK We cordially invite you to submit your contribution to the demo track of the 2010 ACM International Conference on Health Informatics (IHI 2010). The IHI demo track is an exciting and highly interactive way to demonstrate your health informatics system or application. Because of IHI's focus on end-to-end systems, whereby applied informatics is used to address the needs of health and healthcare applications, demos of innovative systems are solicited, which illustrate practical research or engineering contributions in an interesting and interactive manner. The demo program will be featured prominently in the conference program and should be seen as a vehicle for researchers, practitioners, and commercial/industrial/non-profit institutions to showcase innovative new technologies or applications in health informatics. The demo review process will look for practical uses of technology and also for a "wow" factor in all submissions. We encourage the description of early prototypes as long as they clearly present a coherent, end-to-end view of what the application might become once it gets deployed in production. A submission proposal includes a demo paper and can optionally include a demo video, whose URL should be referred to in the textual demo description for reviewers to take into consideration when analyzing the submission. Note that the demo paper should differ from regular papers in several important aspects. First, it should clearly describe the overall architecture of the system or technology demonstrated. Second, the paper should put great emphasis on the motivation of the work, on the applications of the presented system or technology, and on the novelty of the work. Third, the proposal should clearly describe the demo scenario. In particular, it should describe how the demo audience can interact with the demo system, in order to obtain understanding of the underlying technology. For demos running over the web, a back-up scenario should be described, in case of low connectivity at the demo venue. All topics described in the Call for Papers are eligible for demo track submissions. WHAT SHOULD BE SUBMITTED All aspects of the submission and notification process will be handled electronically. Submissions must adhere to the following guidelines: " The author(s) name and affiliation(s) must be present in the submitted document. Any submitted demo proposal violating the length, file type, or formatting requirements will be rejected without review. " Papers must adhere to the ACM Proceedings Format available for LaTex, WordPerfect, WordPerfect 9, and Word. Changing the template's font size, margins, inter-column spacing, or line spacing is prohibited. Each paper must be submitted as a single PDF file, formatted for 8.5" x 11" paper. " The length of submission is 4 pages. This page limit includes all parts of the proposal: title, abstract, body, and bibliography. " Each paper must provide an appendix (which is excluded from the page limit) indicating the preferred review approach, including: - The preferred allocation of reviewing expertise. This can be done by electing the primary and secondary focus of the paper (e.g., Computing, Information Science, Medicine, Nursing, and Social/Behavioral Science). - A bulleted list with up to 3 topics covered in the paper (from the list of conference topics) The optional demo video should focus on illustrating the demo scenario and the interactive nature of the demo system. The video must be no more than three minutes in length and should start by clearly identifying the authors and title of the proposal. The video should be in common video format (e.g., MPEG, AVI), and should be playable on a wide variety of media players. We strongly encourage authors to produce and submit a demo video and such video will be linked off of the final program on the conference website. The notification for acceptance of demo papers is the same as that for regular papers. Accepted demo proposals will appear in the final proceedings and in ACM digital library. Note that all deadlines are the same as for regular paper submissions. IMPORTANT DATES Demo paper submission deadline: June 4, 2010 11:30pm EST Notification of acceptance: August 6, 2010 11:30pm EST Camera-ready copy due: August 16, 2010 11:30pm EST From kiekyon.huang at gmail.com Mon Mar 8 05:53:45 2010 From: kiekyon.huang at gmail.com (kiekyon.huang at gmail.com) Date: Mon, 08 Mar 2010 10:53:45 +0000 Subject: [BiO BB] GC content Message-ID: <0016e64aedec15b527048147e17f@google.com> Hi all, I am looking for materials on the genomic GC content in fungi. Does anybody know of such resources? I had a fungal genome with a genomic GC content of 60%, 60.7% in the coding region, and 58% in the non-coding. Need to compare this with other related fungi. Also, I would like to know what analysis would be more meaningful in this aspect. CpG island or just CpG dinucleotide? thanks a lot! From naveejoshi at gmail.com Mon Mar 8 19:39:58 2010 From: naveejoshi at gmail.com (Naveen Joshi) Date: Tue, 9 Mar 2010 13:39:58 +1300 Subject: [BiO BB] GC content In-Reply-To: <0016e64aedec15b527048147e17f@google.com> References: <0016e64aedec15b527048147e17f@google.com> Message-ID: <15f8051d1003081639p1ebfe3d4n19e2fddaaa454f0b@mail.gmail.com> Hi Kiekyon For obtaining any information about the fungal genes and protein you can refer to the Saccharomyces Genome Database(SGD). If you are not able to find the specific information its always advisable to ask the curators. I am working on the evolution of yeast genes and I also did the same thing when I could not find the information I was looking for. They sent me few links which really helped me a lot. Hope it helps you too. On Mon, Mar 8, 2010 at 11:53 PM, wrote: > Hi all, > > I am looking for materials on the genomic GC content in fungi. Does anybody > know of such resources? > I had a fungal genome with a genomic GC content of 60%, 60.7% in the coding > region, and 58% in the non-coding. Need to compare this with other related > fungi. Also, I would like to know what analysis would be more meaningful in > this aspect. CpG island or just CpG dinucleotide? > > thanks a lot! > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Regards, Naveen Joshi Undergraduate Intern, Computational Evolution Group, University of Auckland, New Zealand 00642102249099 From pkhurana08 at gmail.com Tue Mar 9 01:34:12 2010 From: pkhurana08 at gmail.com (Pankaj Khurana) Date: Tue, 9 Mar 2010 12:04:12 +0530 Subject: [BiO BB] proteins related to a particular disease/condition Message-ID: Hi all, I would like to get a list of all proteins that are upregulated/downregulated during hypoxia. How can I get a list of these proteins? Thanking all in advance Dr. Pankaj Khurana India From skhadar at gmail.com Wed Mar 10 14:42:45 2010 From: skhadar at gmail.com (Khader Shameer) Date: Wed, 10 Mar 2010 13:42:45 -0600 Subject: [BiO BB] proteins related to a particular disease/condition In-Reply-To: References: Message-ID: Hello Pankaj, Have you tried Array Express or HPRD ? -- Khader Shameer On Tue, Mar 9, 2010 at 12:34 AM, Pankaj Khurana wrote: > Hi all, > > I would like to get a list of all proteins that are > upregulated/downregulated during hypoxia. > How can I get a list of these proteins? > > Thanking all in advance > Dr. Pankaj Khurana > India > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From jtcarroll at gmail.com Wed Mar 10 14:46:42 2010 From: jtcarroll at gmail.com (John carroll) Date: Wed, 10 Mar 2010 19:46:42 +0000 Subject: [BiO BB] Bioinformatic workflow software/websites Message-ID: Hi all, I am looking at bioinformatic workflow tools. When looking at a tool i do tutorials/examples, reading papers, etc. I am doing a basic overview of the tools out there, pros & cons, learning curve, usability, etc. Not used any workflow tools before. Looked at these so far: Taverna Galaxy BioExtract Biobike Planning to look at: Ugene Are there other workflow tools i should consider? Thanks -- John Carroll BSc Postgraduate student Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork. Phone:353-21-4326717 From drjohn08318 at yahoo.com Wed Mar 10 14:47:39 2010 From: drjohn08318 at yahoo.com (John G. Hoey, Ph.D.) Date: Wed, 10 Mar 2010 11:47:39 -0800 (PST) Subject: [BiO BB] proteins related to a particular disease/condition Message-ID: <554182.57815.qm@web31813.mail.mud.yahoo.com> Hi Pankaj: I doubt this information has been compiled into a neat little table or list. You will probably have to do a Pubmed search and bring together these data from multiple sources. Also, if you go to www.NCBI.nlm.NIH.gov, select "protein" from the pull-down menu, and search for "hypoxia", you will find a list if proteins shown to be modulated by hypoxia. John John G. Hoey, Ph.D. Sent from my iPhone On Mar 9, 2010, at 1:34, Pankaj Khurana wrote: Hi all, I would like to get a list of all proteins that are upregulated/downregulated during hypoxia. How can I get a list of these proteins? Thanking all in advance Dr. Pankaj Khurana India _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From yvan.saeys at psb.ugent.be Wed Mar 10 15:23:38 2010 From: yvan.saeys at psb.ugent.be (Yvan Saeys) Date: Wed, 10 Mar 2010 21:23:38 +0100 Subject: [BiO BB] Advances in Bio Text Mining - second call for abstracts Message-ID: <4B97FFCA.2070600@psb.ugent.be> ------- Apologies for multiple postings ------- ========================= Second Call for Abstracts ========================= Workshop BioTM-2010: Advances in Bio Text Mining May 10-11, 2010, Ghent, Belgium http://www.clips.ua.ac.be/BioTM2010/index.html ============================================================ Abstracts are invited for the two-day workshop to be held in Ghent on the 10th and 11th of May 2010. Participants are encouraged to submit an extended abstract to the workshop. Authors of selected abstracts will present their work in a five minute bullet talk and their posters will be presented in a poster session. Submitted abstracts will be reviewed by the organising committee. The best abstracts will be published in an abstract supplement of BMC Bioinformatics (http://www.biomedcentral.com/bmcbioinformatics/). Submission deadline: April 1, 2010. ============================================================ The program of the workshop includes: - an extensive tutorial on Bio Text Mining by Martin Krallinger - invited talks by leading scientists in the field: Sampo Pyysalo, Kevin Cohen and Filip Ginter - invited talks by experienced scientists from industry: Jean-Marc Neefs, Luc Dehaspe and Mat? Ongenaert ============================================================ Text mining has become indispensible in many biological and biomedical sciences. Having to keep up with an increasing number of publications, text mining techniques enable retrieval and analysis of large amounts of documents in a fully automated fashion. They allow for extraction of facts described in the literature that have not yet been recorded in databases, thus providing a necessary tool to obtain a complete overview of all available knowledge. Recently, the application of text mining and natural language processing techniques to the biological and medical sciences has recieved increasing interest. In addition to many new workshops and conferences arising in this domain, recently also a number of community-wide tasks were conducted to benchmark text mining techniques on specific challenges (e.g. BioCreative, BioNLP Shared Task, ...). By discussing the latest developments and potentially new applications in text mining amongst scientists in both academia and industry, this workshop aims to provide a broad view on text mining tools in biology and biomedicine. We are reaching out to a broad public, including researchers with an interest in text mining but with little or no experience in this domain. To this end, the workshop will start with an extensive tutorial on text mining in the bio-sciences, providing sufficient background knowledge for novices. Next, a number of keynote talks will be given by leading scientists, presenting the latest advances in the field. Furthermore, participants are highly encouraged to submit an abstract describing their own work. They will be given the opportunity to present this work in 5min flash presentations, as well as to present a poster during the coffee and lunch breaks. Finally, we plan on having a round-table discussion about the broader applicability of text-mining tools in the biological sciences, trying to bridge the gap between theoretical algorithms and experimental work. ============================================================ SUBMISSIONS: SCOPE Submissions should present work related to any aspect of biomedical text mining and bioinformatics. Additionally, we strongly encourage submissions that describe shortcomings of current existing techniques, tools, or resources, in order to detect problematic issues and work towards their improvement. SUBMISSIONS: INSTRUCTIONS An abstract of maximum 400 words with at most 1 table or figure should be submitted to the following e-mail address in pdf format: biotm2010 at gmail dot com Detailed formatting instructions can be found at http://www.clips.ua.ac.be/BioTM2010/call.html Submission is blind. ============================================================ IMPORTANT DATES 1 April 2010 Submission deadline 15 April 2010 Notification of acceptance 30 April 2010 Camera-ready abstracts due 10-11 May 2010 Workshop in Ghent ============================================================ ORGANISATION / PROGRAM COMMITTEE Yvan Saeys Thomas Abeel Sofie Van Landeghem Bioinformatics and Evolutionary Genomics group VIB Department of Plant Systems Biology Ghent University, Belgium Walter Daelemans Roser Morante Vincent Van Asch CLiPS - Text Mining Group Faculty of Arts University of Antwerp, Belgium -- ================================================================== Dr. Yvan Saeys, PhD DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 331 38 09 BIOINFORMATICS TEAM Tel:32 (0)9 331 36 95 GHENT UNIVERSITY, Technologiepark 927, B-9052 Gent, Belgium Vlaams Instituut voor Biotechnologie VIB mailto:yvan.saeys at ugent.be http://bioinformatics.psb.ugent.be/ http://www.psb.ugent.be/~yvsae/ ================================================================== From marchywka at hotmail.com Wed Mar 10 16:59:20 2010 From: marchywka at hotmail.com (Mike Marchywka) Date: Wed, 10 Mar 2010 16:59:20 -0500 Subject: [BiO BB] proteins related to a particular disease/condition In-Reply-To: <554182.57815.qm@web31813.mail.mud.yahoo.com> References: <554182.57815.qm@web31813.mail.mud.yahoo.com> Message-ID: I think one of the pubmed? DB's is something about expression array submissions in computer readable form. That would probably be your best bet for data compilation. I guess you could also take empirical observations and chase them through pathway DB;s for logical consequences ( if A goes up then B must go up etc). I don't think you will find a numerically accurate cell diagram with an oxygen sensor and connections therefrom LOL. Let me know what you do find however as I'm working on some forums for letting people collate fuzzy stuff like this. When I say fuzzy, "hypoxia" per se is not a complete environmental or state specification and "your mileage may vary" depending on the other state variables of the cell. I do a lot of this kind of thing with barely structured documents. I just got done trying to pull out peptide sequences from abstracts based on regular expressions. Still not sure how well I did but I guess you could download all the abstracts that mention hypoxia and regulation and then remove common words and see what you have left. Run the uncommon words against the pubmed protein DB and if they come up you probably have a protein name that has some relevance to your serch criteria. ---------------------------------------- > Date: Wed, 10 Mar 2010 11:47:39 -0800 > From: drjohn08318 at yahoo.com > To: bbb at bioinformatics.org > CC: bbb at bioinformatics.org > Subject: Re: [BiO BB] proteins related to a particular disease/condition > > Hi Pankaj: > I doubt this information has been compiled into a neat little table or list. You will probably have to do a Pubmed search and bring together these data from multiple sources. Also, if you go to www.NCBI.nlm.NIH.gov, select "protein" from the pull-down menu, and search for "hypoxia", you will find a list if proteins shown to be modulated by hypoxia. > John > > > John G. Hoey, Ph.D. > > Sent from my iPhone > > On Mar 9, 2010, at 1:34, Pankaj Khurana wrote: > > Hi all, > > I would like to get a list of all proteins that are > upregulated/downregulated during hypoxia. > How can I get a list of these proteins? > > Thanking all in advance > Dr. Pankaj Khurana > India > _______________________________________________ note new address Mike Marchywka 1975 Village Round Marietta GA 30064 415-264-8477 (w)<- use this 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/201469229/direct/01/ From tirza at biomodel.os.biu.ac.il Thu Mar 11 03:55:07 2010 From: tirza at biomodel.os.biu.ac.il (Tirza Doniger) Date: Thu, 11 Mar 2010 10:55:07 +0200 Subject: [BiO BB] proteins related to a particular disease/condition In-Reply-To: References: Message-ID: Hi Pankaj, Have you tried http://www.genecards.org/? I know they have information about disease related genes. Best, Tirza On Tue, Mar 9, 2010 at 8:34 AM, Pankaj Khurana wrote: > Hi all, > > I would like to get a list of all proteins that are > upregulated/downregulated during hypoxia. > How can I get a list of these proteins? > > Thanking all in advance > Dr. Pankaj Khurana > India > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Tirza Doniger, M.Sc. PhD student Laboratory of Prof. Ron Unger Laboratory of Computational Biology Bar Ilan University ====================== Life is like riding a bicycle. To keep your balance you must keep moving. -----Albert Einstein From svtrived at hotmail.com Thu Mar 11 09:21:39 2010 From: svtrived at hotmail.com (Seema Trivedi) Date: Thu, 11 Mar 2010 19:51:39 +0530 Subject: [BiO BB] GC content In-Reply-To: <15f8051d1003081639p1ebfe3d4n19e2fddaaa454f0b@mail.gmail.com> References: <0016e64aedec15b527048147e17f@google.com>, <15f8051d1003081639p1ebfe3d4n19e2fddaaa454f0b@mail.gmail.com> Message-ID: Hi If you are looking for CG content of the genomes, you can try NCBI complete genome page. The complete genome page browsing will take you to the genome project pages (at times or else the statistics of the genome). This is where you can get the total no. of genes, total no. of protein coding genes, RNA coding genes etc. besides the CG content of the genome. Moreover, there are no. of software that can help you calculate CG content of a sequence. I can try relocating the names of those in case NCBI is not of help (which I am sure will provide information that you need). Else you can write a small perl script to do it for you. S Trivedi > Date: Tue, 9 Mar 2010 13:39:58 +1300 > From: naveejoshi at gmail.com > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] GC content > > Hi Kiekyon > > For obtaining any information about the fungal genes and protein you > can refer to the Saccharomyces Genome Database(SGD). If you are not able to > find the specific information its always advisable to ask the curators. I am > working on the evolution of yeast genes and I also did the same thing when I > could not find the information I was looking for. They sent me few links > which really helped me a lot. > > Hope it helps you too. > > On Mon, Mar 8, 2010 at 11:53 PM, wrote: > > > Hi all, > > > > I am looking for materials on the genomic GC content in fungi. Does anybody > > know of such resources? > > I had a fungal genome with a genomic GC content of 60%, 60.7% in the coding > > region, and 58% in the non-coding. Need to compare this with other related > > fungi. Also, I would like to know what analysis would be more meaningful in > > this aspect. CpG island or just CpG dinucleotide? > > > > thanks a lot! > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > -- > Regards, > > Naveen Joshi > Undergraduate Intern, > Computational Evolution Group, > University of Auckland, > New Zealand > 00642102249099 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Green cities and the melting world http://green.in.msn.com/ From svtrived at hotmail.com Thu Mar 11 09:25:26 2010 From: svtrived at hotmail.com (Seema Trivedi) Date: Thu, 11 Mar 2010 19:55:26 +0530 Subject: [BiO BB] proteins related to a particular disease/condition In-Reply-To: <554182.57815.qm@web31813.mail.mud.yahoo.com> References: <554182.57815.qm@web31813.mail.mud.yahoo.com> Message-ID: Yes, John G. Hoey is correct in giving the information. I would like to add that the NCBI protein pulldown and search term hypoxia will take you the page that will give you the list of proteins/genes. Then you can trim the information through the advance search or limits tab if you want it to be genome specific or whatever choises that are available. S Trivedi > Date: Wed, 10 Mar 2010 11:47:39 -0800 > From: drjohn08318 at yahoo.com > To: bbb at bioinformatics.org > CC: bbb at bioinformatics.org > Subject: Re: [BiO BB] proteins related to a particular disease/condition > > Hi Pankaj: > I doubt this information has been compiled into a neat little table or list. You will probably have to do a Pubmed search and bring together these data from multiple sources. Also, if you go to www.NCBI.nlm.NIH.gov, select "protein" from the pull-down menu, and search for "hypoxia", you will find a list if proteins shown to be modulated by hypoxia. > John > > > John G. Hoey, Ph.D. > > Sent from my iPhone > > On Mar 9, 2010, at 1:34, Pankaj Khurana wrote: > > Hi all, > > I would like to get a list of all proteins that are > upregulated/downregulated during hypoxia. > How can I get a list of these proteins? > > Thanking all in advance > Dr. Pankaj Khurana > India > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ What does Budget 2010 mean for you? Catch all the latest news, updates and analysis on MSN Budget Special http://news.in.msn.com/moneyspecial/budget2010 From svtrived at hotmail.com Thu Mar 11 09:27:21 2010 From: svtrived at hotmail.com (Seema Trivedi) Date: Thu, 11 Mar 2010 19:57:21 +0530 Subject: [BiO BB] proteins related to a particular disease/condition In-Reply-To: <554182.57815.qm@web31813.mail.mud.yahoo.com> References: <554182.57815.qm@web31813.mail.mud.yahoo.com> Message-ID: Hi once again In addition to the NCBI you can try to Gene Ontology GO (or Amigo) database. From here you can give the search term, get either the protein/gene IDs or GO Ids. These IDs can then be searched at NCBI or SwissProt. S Trivedi > Date: Wed, 10 Mar 2010 11:47:39 -0800 > From: drjohn08318 at yahoo.com > To: bbb at bioinformatics.org > CC: bbb at bioinformatics.org > Subject: Re: [BiO BB] proteins related to a particular disease/condition > > Hi Pankaj: > I doubt this information has been compiled into a neat little table or list. You will probably have to do a Pubmed search and bring together these data from multiple sources. Also, if you go to www.NCBI.nlm.NIH.gov, select "protein" from the pull-down menu, and search for "hypoxia", you will find a list if proteins shown to be modulated by hypoxia. > John > > > John G. Hoey, Ph.D. > > Sent from my iPhone > > On Mar 9, 2010, at 1:34, Pankaj Khurana wrote: > > Hi all, > > I would like to get a list of all proteins that are > upregulated/downregulated during hypoxia. > How can I get a list of these proteins? > > Thanking all in advance > Dr. Pankaj Khurana > India > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Fight for the top Test spot http://sports.in.msn.com/cricket/ From clements at nescent.org Thu Mar 11 13:43:48 2010 From: clements at nescent.org (Dave Clements) Date: Thu, 11 Mar 2010 10:43:48 -0800 Subject: [BiO BB] Bioinformatic workflow software/websites In-Reply-To: References: Message-ID: Hi John, Kepler (https://kepler-project.org/) is another workflow system. I believe Kepler is particularly popular in evolutionary biology. Another option is Ergatis (http://ergatis.sourceforge.net/), which is currently seeing a lot of development to make it be cloud enabled. Dave C On Wed, Mar 10, 2010 at 11:46 AM, John carroll wrote: > Hi all, > > I am looking at bioinformatic workflow tools. > When looking at a tool i do tutorials/examples, reading papers, etc. > I am doing a basic overview of the tools out there, pros & cons, learning > curve, usability, etc. Not used any workflow tools before. > > Looked at these so far: > Taverna > Galaxy > BioExtract > Biobike > > Planning to look at: > Ugene > > Are there other workflow tools i should consider? > > Thanks > > -- > John Carroll BSc > Postgraduate student > Department of Biological Sciences, > Cork Institute of Technology, > Bishopstown, Cork. > Phone:353-21-4326717 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- http://gmod.org/wiki/GMOD_Logo_Program http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/Help_Desk_Feedback From silaslabedo at gmail.com Fri Mar 12 02:10:57 2010 From: silaslabedo at gmail.com (Silas Labedo) Date: Fri, 12 Mar 2010 10:10:57 +0300 Subject: [BiO BB] CD-HIT Support Request Message-ID: <4B99E901.2090600@i-a-inc.com> Hi Everyone, I am writing a clustering program in java that calls cd-hit for New, Incremental, and Hierarchical clustering. The program works fine for New clustering, however when I attempt to call cd-hit from within the java code for Incremental clustering, I get errors. The error logs are attached below. 3 different errors occured that I don't understand and are the reason for which I am seeking your assistance. This error occurred when trying to execute cd-hit for hierarchical clustering from the linux command prompt. **************************************************************************************** [root at ip-10-194-215-223 cd-hit]# ./psi-cd-hit-local.pl -i hierarchical93 -o hierarchical90 -c 0.90 Name "main::formatdb_no" used only once: possible typo at ./psi-cd-hit-local.pl line 1712. Name "main::known_singles" used only once: possible typo at ./psi-cd-hit-local.pl line 1873. Name "main::longest_ide" used only once: possible typo at ./psi-cd-hit-local.pl line 966. Name "main::known_single" used only once: possible typo at ./psi-cd-hit-local.pl line 1873. [root at ip-10-194-215-223 cd-hit]# [root at ip-10-194-215-223 cd-hit]# perl psi-cd-hit.pl -i hierarchical93 -o hierarchical90 -c 0.3 Name "main::reformat_seg" used only once: possible typo at psi-cd-hit.pl line 65. Name "main::restart_seg" used only once: possible typo at psi-cd-hit.pl line 62. Can't exec "formatdb": No such file or directory at .//psi-cd-hit-local.pl line 1723. Can not formatdb at .//psi-cd-hit-local.pl line 1724. [root at ip-10-194-215-223 cd-hit]# vi hierarchical90.log [root at ip-10-194-215-223 cd-hit]# vi hierarchical90.out [root at ip-10-194-215-223 cd-hit]# The following outputs and subsequent errors occurred during incremental clustering executed from within a java code. **************************************************************************************** Cluster CMD: C:\cd-hit-windows\cd_hit_2d.exe -i "C:/cluster files/unipath_2010-3-9.clstr" -i2 "c:/cluster files/unipath_2010-3-9.fasta" -o "C:/cluster files/unipath_2010-3-9" -c 0.9 -n 5 -d 50 Mar 9, 2010 6:55:31 AM Here is the standard output of the command: total seq in db1: 0 total seq in db2: 15732 longest and shortest : 0 and 99999999 Total letters: 0 Mar 9, 2010 6:55:57 AM Process Exit Value : 1 Mar 9, 2010 6:55:57 AM Here is the standard error of the command (if any): Fatal Error Memory Program halted !! ************************************************************************************** Cluster CMD: C:\cd-hit-windows\cd_hit_2d.exe -i "C:/cluster files/clusteroutput.clstr" -i2 "c:/cluster files/aric_2010-3-10.fasta" -o "C:/cluster files/aric_2010-3-10" -c 0.9 -n 5 -d 50 Mar 10, 2010 6:51:01 AM Here is the standard output of the command: total seq in db1: 79 total seq in db2: 4776 longest and shortest : 48 and 11 Total letters: 1061 Sequences have been sorted longest and shortest : 34350 and 11 Total letters: 3167574 compute index table for first database Reading swap Comparing with SEG 0 ..........1000 compared 0 clustered ..........2000 compared 0 clustered ..........3000 compared 0 clustered ..........4000 compared 0 clustered ....... 4776 compared 0 clustered writing non-redundant sequences from db2 writing clustering information program completed ! Total CPU time 103 Mar 10, 2010 6:51:23 AM Process Exit Value : 0 Mar 10, 2010 6:51:23 AM Here is the standard error of the command (if any): The attached fasta file was generated along with the last part of the output/error log. The contents of the fasta file are very un-familiar and I would be very grateful if someone can help me understand it. Thanks you all. Regards. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: aric_2010-3-10.clstr URL: From nilanjanag08 at gmail.com Sat Mar 13 14:30:15 2010 From: nilanjanag08 at gmail.com (Nilanjana Gangopadhyay) Date: Sun, 14 Mar 2010 01:00:15 +0530 Subject: [BiO BB] Problem in MAKEMAT in PSIPRED Message-ID: Dear Members, Currently I am working on protein secondary structure prediction using neural network. I was using PSIPRED but I am getting error: [makematrices] FATAL ERROR : unable to open file psitmp68765db92331.chk I am sending my script for your reference: #!/bin/tcsh # This is a simple script which will carry out all of the basic steps # required to make a PSIPRED V2 prediction. Note that it assumes that the # following programs are in the appropriate directories: # blastpgp - PSIBLAST executable (from NCBI toolkit) # makemat - IMPALA utility (from NCBI toolkit) # psipred - PSIPRED V2 program # psipass2 - PSIPRED V2 program # NOTE: Script modified to be more cluster friendly (DTJ April 2008) # The name of the BLAST data bank set dbname = nr.fasta # set dbname = nr # Where the NCBI programs have been installed set ncbidir = ./binblast # set ncbidir = C:/cygwin/usr/local/bin # Where the PSIPRED V2 programs have been installed set execdir = ./bin # Where the PSIPRED V2 data files have been installed set datadir = ./data set basename = $1:r set rootname = $basename:t # Generate a "unique" temporary filename root set hostid = `hostid` set tmproot = psitmp$$$hostid \cp -f $1 $tmproot.fasta echo "Running PSI-BLAST with sequence" $1 "..." #$ncbidir/blastpgp -b 0 -j 3 -h 0.001 -d $dbname -i $tmproot.fasta -C $tmproot.chk >& $tmproot.blast $ncbidir/blastpgp -b 0 -j 3 -h 0.001 -d $dbname -i $tmproot.fasta -C $tmproot.chk echo "Predicting secondary structure..." echo $tmproot.chk > $tmproot.pn echo $tmproot.fasta > $tmproot.sn $ncbidir/makemat -P $tmproot echo Pass1 ... $execdir/psipred $tmproot.mtx $datadir/weights.dat $datadir/weights.dat2 $datadir/weights.dat3 $datadir/weights.dat4 > $rootname.ss echo Pass2 ... $execdir/psipass2 $datadir/weights_p2.dat 1 1.0 1.0 $rootname.ss2 $rootname.ss > $rootname.horiz # Remove temporary files echo Cleaning up ... #\rm -f $tmproot.* error.log echo "Final output files:" $rootname.ss2 $rootname.horiz echo "Finished." I am running the script using Putty. Though that makemat -P test.chk command is running fine in command prompt. .mtx file is also generated. and .chk files are also generated when I am running blastpgp and makemat separately. Any help will be greatly thanked. -- Thanking You, Yours Truly, Nilanjana G @+40 749527113 From maximilianh at gmail.com Sun Mar 14 10:51:04 2010 From: maximilianh at gmail.com (Maximilian Haussler) Date: Sun, 14 Mar 2010 14:51:04 +0000 Subject: [BiO BB] proteins related to a particular disease/condition In-Reply-To: References: Message-ID: <76f031ae1003140751n1d90d648x97eed6a2177d9814@mail.gmail.com> I assume that you either have to read papers for this (google: microarray hypoxia upregulated genes) and then get their supplemental data or do bit of digging in NCBI GEO. Here is a hypoxia dataset in geo that I've found by searching geo for hypoxia: http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE3188 I think nextbio has already processed the data in the way that you need but it's a company and I don't know which part you can use for free is you're a researcher: http://www.nextbio.com/b/search/disc.nb?q=hypoxic#cat=Genes good luck Max -- Maximilian Haussler Tel: +447542993736 +447574054746 http://www.ls.manchester.ac.uk/people/profile/index.asp?id=4774 On Tue, Mar 9, 2010 at 6:34 AM, Pankaj Khurana wrote: > Hi all, > > I would like to get a list of all proteins that are > upregulated/downregulated during hypoxia. > How can I get a list of these proteins? > > Thanking all in advance > Dr. Pankaj Khurana > India > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From drjohn08318 at yahoo.com Sun Mar 14 15:28:33 2010 From: drjohn08318 at yahoo.com (John G. Hoey, Ph.D.) Date: Sun, 14 Mar 2010 12:28:33 -0700 (PDT) Subject: [BiO BB] proteins related to a particular disease/condition Message-ID: <268108.33113.qm@web31801.mail.mud.yahoo.com> Unless I'm mistaken, Pankaj had asked for sources on up and down-regulated proteins, not genes. I frequently make use of the information in the Geo datasets to target genes encoding proteins whose expression might be changed under a set of experimental conditions. However, it is important to keep in mind there is often no correlation between changes in gene expression (as presented in such microarray datasets) and protein levels. As long as these caveats are kept in mind, such datasets represent a good jumping off point for identifying proteins of potential relevance to your particular experiment. John John G. Hoey, Ph.D. Sent from my iPhone On Mar 14, 2010, at 10:51, Maximilian Haussler wrote: I assume that you either have to read papers for this (google: microarray hypoxia upregulated genes) and then get their supplemental data or do bit of digging in NCBI GEO. Here is a hypoxia dataset in geo that I've found by searching geo for hypoxia: http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE3188 I think nextbio has already processed the data in the way that you need but it's a company and I don't know which part you can use for free is you're a researcher: http://www.nextbio.com/b/search/disc.nb?q=hypoxic#cat=Genes good luck Max -- Maximilian Haussler Tel: +447542993736 +447574054746 http://www.ls.manchester.ac.uk/people/profile/index.asp?id=4774 On Tue, Mar 9, 2010 at 6:34 AM, Pankaj Khurana wrote: Hi all, I would like to get a list of all proteins that are upregulated/downregulated during hypoxia. How can I get a list of these proteins? Thanking all in advance Dr. Pankaj Khurana India _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From cannataro at unicz.it Sun Mar 14 17:53:03 2010 From: cannataro at unicz.it (Mario Cannataro) Date: Sun, 14 Mar 2010 22:53:03 +0100 (CET) Subject: [BiO BB] Euro-Par Workshop on High Performance Bioinformatics and Biomedicine (HiBB) Message-ID: <72c4ffffd120634dccdde189790e4eb7.squirrel@email.unicz.it> I apologize for any cross-posting of this announcement. ===================================================================== Euro-Par 2010 Ischia, Naples, Italy August 31 - September 3, 2010 1st Workshop on High Performance Bioinformatics and Biomedicine (HiBB) http://staff.icar.cnr.it/cannataro/hibb2010/ ===================================================================== * * * CALL FOR PAPERS - Deadline April 16, 2010 * * * ===================================================================== High-throughput technologies (e.g. microarray and mass spectrometry) and clinical diagnostic tools (e.g. medical imaging) are producing an increasing amount of experimental and clinical data. In such a scenario, large scale databases and bioinformatics tools are key tools for organizing and exploring biological and biomedical data with the aim to discover new knowledge in biology and medicine. High-performance computing may play an important role in many phases of life sciences research, from raw data management and processing, to data analysis and integration, till data exploration and visualization. In particular, at the raw data layer, Grid infrastructures may offer the huge data storage needed to store experimental and biomedical data, while parallel computing can be used for basic pre-processing (e.g. parallel BLAST) and for more advanced analysis (e.g. parallel data mining). In such a scenario, novel parallel architectures (e.g. e.g. CELL processors, GPUs, FPGA, hybrid CPU/FPGA) coupled with emerging programming models may overcome the limits posed by conventional computers to the mining and exploration of large amounts of data. At an higher layer, emerging biomedical applications need to use in a coordinated way both bioinformatics tools, biological data banks and patient?s clinical data, that require seamless integration, privacy preservation and controlled sharing. Service Oriented Architectures and semantic technologies, such as ontologies, may allow the building and deployment of the so called ?collaboratories?, where experimental research may be conducted by remote scientists in a collaborative way. The goal of HiBB is to bring together scientists in the fields of high performance computing, computational biology and medicine to discuss, among the others, the organization of large scale biological and biomedical databases and the parallel implementation of bioinformatics algorithms and biomedical applications. Furthermore, the use of novel parallel architectures and dedicated hardware to implement bioinformatics and biomedical algorithms will be discussed. TOPICS OF INTEREST The workshop is seeking original research papers presenting applications of parallel and high performance computing to biology and medicine. Topics of interest include, but are not limited to: - Large scale biological and biomedical databases - Data integration and ontologies in biology and medicine - Parallel bioinformatics algorithms - Parallel visualization and exploration of biomedical data - Parallel visualization and analysis of biomedical images - Computing environments for large scale collaboration - Scientific workflows in bioinformatics and biomedicine - (Web) Services for bioinformatics and biomedicine - Grid Computing for bioinformatics and biomedicine - Peer-To-Peer Computing for bioinformatics and biomedicine - Emerging architectures and programming models (e.g. Cell, GPUs) for bioinformatics and biomedicine - Parallel processing of bio-signals - Modeling and simulation of complex biological processes PAPER SUBMISSION AND PUBLICATION We invite original previously unpublished contributions. Full papers should not exceed 12 pages in the Springer LNCS style. Paper submission has to be performed by sending the PDF file to the workshop chair: cannataro AT unicz.it Papers accepted for publication must also be supplied in source form (Latex or Word). All accepted papers will be included in the Workshops proceedings, that will be published in a separate Springer LNCS Euro-Par 2010 Workshop volume after the conference. Authors of accepted papers will be required to sign up a Springer copyright form.. JOURNAL SPECIAL ISSUE At the end of the workshop, we plan to invite the best 4-6 papers of the workshop for a special section on an international journal. IMPORTANT DATES Full papers submission: April 16, 2010 Decision Notification: May 17, 2010 Camera ready papers: June 1, 2010 Workshop sessions : August 30-31, 2010 WORKSHOP ORGANIZER Mario Cannataro, University Magna Gr?cia of Catanzaro, Italy PROGRAM COMMITTEE (TO BE CONFIRMED) 1. Pratul K. Agarwal, Oak Ridge National Laboratory, USA 2. David A. Bader, College of Computing, Georgia University of Technology, USA 3. Ignacio Blanquer; Universidad Polit?cnica de Valencia, Valencia, Spain 4. Daniela Calvetti, Case Western Reserve University, USA 5. Werner Dubitzky, University of Ulster, UK 6. Ananth Y. Grama, Purdue University, USA 7. Concettina Guerra, University of Padova, Italy 8. Vicente Hern?ndez, Univ. Polit?cnica de Valencia, Spain 9. Salvatore Orlando, University of Venezia, Italy 10. Omer F. Rana, Cardiff University, UK 11. Richard Sinnott; National e-Science Centre, University of Glasgow, United Kingdom 12. Fabrizio Silvestri, ISTI-CNR, Italy 13. Erkki Somersalo, Case Western Reserve University, USA 14. Paolo Trunfio, University of Calabria, Italy 15. Albert Zomaya, University of Sydney, Australia **************************************** Prof. Mario Cannataro, Informatics and Biomedical Engineering, University "Magna Gr?cia" of Catanzaro, Viale Europa (Localit? Germaneto), 88100 CATANZARO, ITALY, Tel: 0961-369 4100, Fax: 0961-369 4073/4090, Email: cannataro at unicz.it, Web: http://bioingegneria.unicz.it/~cannataro/ **************************************** New book release Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare ISBN: 978-1-60566-374-6; 1,050 pp; May 2009 Published under Medical Information Science Reference an imprint of IGI Global http://www.igi-global.com/reference/details.asp?id=34292 Edited by: Mario Cannataro, University Magna Graecia of Catanzaro, Italy **************************************** From kiekyon.huang at gmail.com Mon Mar 15 01:22:36 2010 From: kiekyon.huang at gmail.com (Kie Kyon Huang) Date: Mon, 15 Mar 2010 13:22:36 +0800 Subject: [BiO BB] TRIBE-MCL cllustering tool Message-ID: Anyone familiar with the steps to cluster protein family using tribe-MCL I was trying to follow the instruction at http://biocourse.org/index.php/TribeMCL but it seems that many programs are not provided? Thanks From rafik at ubuntu.com Mon Mar 15 11:57:34 2010 From: rafik at ubuntu.com (Rafik Ouerchefani) Date: Mon, 15 Mar 2010 16:57:34 +0100 Subject: [BiO BB] protein merge Message-ID: Hello, I'm looking for a software that can merge two proteins with a shared domain (given .pdb files). With sequences it would be like this : seq 1 : MSARIATRRRDKKARRKLQ*ELGATRLVVHRT* seq 2 : *ELGATRLVVHRT*PRHIYAPNGSEVLVQVIAA result : MSARIATRRRDKKARRKLQ*ELGATRLVVHRT*PRHIYAPNGSEVLVQVIAA These two sequences have a common sequence ELGATRLVVHRT (end of the first and beginning of the second). It's easy with sequences but I have to do it with 3D structures. I have the 3D structures of both sequences 1 and 2. Thanks, - Rafik From dan.bolser at gmail.com Mon Mar 15 13:21:07 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 15 Mar 2010 17:21:07 +0000 Subject: [BiO BB] protein merge In-Reply-To: References: Message-ID: <2c8757af1003151021t516c3b26mf7c825bbc13e3a57@mail.gmail.com> Isn't this just sequence (or structure) alignment? The consensus would then be the merged sequence. You should be able to find lots of alignment tools out there. On 15 March 2010 15:57, Rafik Ouerchefani wrote: > > Hello, > > I'm looking for a software that can merge two proteins with a shared domain > (given .pdb files). > With sequences it would be like this : > > seq 1 : ?MSARIATRRRDKKARRKLQ*ELGATRLVVHRT* > seq 2 : ?*ELGATRLVVHRT*PRHIYAPNGSEVLVQVIAA > result : MSARIATRRRDKKARRKLQ*ELGATRLVVHRT*PRHIYAPNGSEVLVQVIAA > > These two sequences have a common sequence ELGATRLVVHRT (end of the first > and beginning of the second). It's easy with sequences but I have to do it > with 3D structures. I have the 3D structures of both sequences 1 and 2. > > Thanks, > > - Rafik > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From naveejoshi at gmail.com Mon Mar 15 16:07:36 2010 From: naveejoshi at gmail.com (Naveen Joshi) Date: Tue, 16 Mar 2010 09:07:36 +1300 Subject: [BiO BB] protein merge In-Reply-To: <2c8757af1003151021t516c3b26mf7c825bbc13e3a57@mail.gmail.com> References: <2c8757af1003151021t516c3b26mf7c825bbc13e3a57@mail.gmail.com> Message-ID: <15f8051d1003151307o25304042x8c1db7a71c0849b3@mail.gmail.com> Hi Rafik Hi think you are trying to study the gene fusion event or the duplication of a specific part of protein due to gene duplication.. Maybe you can try reading some papers on the phenomenon of gene fusion. try going for a review paper as they list all the important techniques ans also software to analyse such instances which people have used throughout the years .. On Tue, Mar 16, 2010 at 6:21 AM, Dan Bolser wrote: > Isn't this just sequence (or structure) alignment? > > The consensus would then be the merged sequence. > > You should be able to find lots of alignment tools out there. > > > > On 15 March 2010 15:57, Rafik Ouerchefani wrote: > > > > Hello, > > > > I'm looking for a software that can merge two proteins with a shared > domain > > (given .pdb files). > > With sequences it would be like this : > > > > seq 1 : MSARIATRRRDKKARRKLQ*ELGATRLVVHRT* > > seq 2 : *ELGATRLVVHRT*PRHIYAPNGSEVLVQVIAA > > result : MSARIATRRRDKKARRKLQ*ELGATRLVVHRT*PRHIYAPNGSEVLVQVIAA > > > > These two sequences have a common sequence ELGATRLVVHRT (end of the first > > and beginning of the second). It's easy with sequences but I have to do > it > > with 3D structures. I have the 3D structures of both sequences 1 and 2. > > > > Thanks, > > > > - Rafik > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Regards, Naveen Joshi Undergraduate Intern, Computational Evolution Group, University of Auckland, New Zealand 00642102249099 From jigar.halani at wipro.com Mon Mar 15 13:58:56 2010 From: jigar.halani at wipro.com (jigar.halani at wipro.com) Date: Mon, 15 Mar 2010 23:28:56 +0530 Subject: [BiO BB] 17th IEEE International Conference on High Performance Computing Message-ID: ********************************************************************** C A L L F O R P A P E R S 17th IEEE International Conference on High Performance Computing (HiPC 2010) December 19-22, 2010 Goa, INDIA http://www.hipc.org Paper Submission Deadline: May 15, 2010 ********************************************************************** IMPORTANT DATES April 04, 2010 Conference Paper Submission Begins May 15, 2010 Conference Paper Submission Ends May 15, 2010 Workshop Proposals Due May 18, 2010 Tutorial Proposals Due July 17, 2010 Notification of Acceptance/Rejection Aug 17, 2010 Camera-Ready Paper Submission Sep 14, 2010 Student Symposium Submissions Due Oct 19, 2010 Student Symposium Accept/Reject Decisions Nov 09, 2010 Early Registration Deadline ----------------------------------------------------------------------------- The 17th annual IEEE International Conference on High Performance Computing (HiPC 2010) will be held in Goa, India, during December 19-22, 2010. It will serve as a forum for researchers from around the world to present their current research efforts and findings, and will act as a venue for stimulating discussions and for highlighting high performance computing (HPC) activities in Asia. The conference has a history of attracting participation from reputed researchers from all over the world. HiPC 2010 will focus on the design and analysis of high performance computing and networking systems and their scientific, engineering, and commercial applications. In addition to technical sessions consisting of contributed papers, the conference will include invited presentations, a student research symposium, tutorials, and vendor presentations The 16th meeting, held in Kochi, India in December 2009, had 49 contributed papers that were selected from 261 submissions from 20 countries, and about 225 participants attended the meeting. The 15th meeting, held in Bangalore, India in December 2008, had 46 contributed papers that were selected from over 317 submissions and approximately 250 participants attended the meeting. The 14th meeting, held in Goa, India in December 2007, had 52 contributed papers that were selected from over 253 submissions from 31 countries and approximately 300 participants attended the meeting. The HiPC attendance is approximately 300 with a good mix of participants from India and the rest of the world. Further information about HiPC 2010 and the HiPC series of meetings is available on the conference website at http://www.hipc.org. ----------------------------------------------------------------------------- CO-SPONSORED BY: * IEEE Computer Society Technical Committee on Parallel Processing (TCPP) - Pending * HiPC Education Trust IN COOPERATION WITH: * ACM SIGARCH - Pending ----------------------------------------------------------------------------- VENUE AND MEETING INFORMATION HiPC will be held at the Cidade-de-Goa, Goa, India (http://cidadedegoa.com/). The advance program will be available in July 2010. Please check the conference website at http://www.hipc.org for updated information. ----------------------------------------------------------------------------- ======================= HiPC 2010 CALL FOR PAPERS ======================= Authors are invited to submit original unpublished manuscripts that demonstrate current research in all areas of high performance computing including design and analysis of parallel and distributed systems, embedded systems, and their applications in scientific, engineering, and commercial areas. Topics of interest include but are not limited to: * High-Performance Computing * Parallel and Distributed Algorithms * Parallel Languages and Programming Environments * Load Balancing, Scheduling and Resource Management * Resilient/Fault-Tolerant Algorithms and Systems * Scientific/Engineering/Commercial Applications and Workloads * Emerging Applications such as Biotechnology and Nanotechnology * Cluster, Cloud, and Grid Cloud Computing * Peer-to-peer Algorithms and Networks * Heterogeneous Computing * Wireless and Mobile Computing * Communication/Sensor Networks and Embedded Applications * Interconnection Networks and Architectures * Scalable Servers and Systems * High Performance/Scalable Storage Systems * Power-Efficient and Reconfigurable Architectures * Compiler Technologies for High-Performance Computing * Software Support and Advanced Micro-architecture Techniques * Operating Systems for Scalable High-Performance Computing ----------------------------------------------------------------------------- MANUSCRIPT GUIDELINES Submitted manuscripts should be structured as technical papers and may not exceed 10 letter size (8.5 x 11) pages including figures, tables and references using the IEEE format for conference proceedings (print area of 6-1/2 inches (16.51 cm) wide by 8-7/8 inches (22.51 cm) high, two-column format with columns 3-1/16 inches (7.85 cm) wide with a 3/8 inch (0.81 cm) space between them, single-spaced 10-point Times fully justified text). Submissions not conforming to these guidelines may be returned without review. Authors should submit the manuscript in PDF format and make sure that the file will print on a printer that uses letter size (8.5 x 11) paper. The official language of the meeting is English. Manuscript submission will start on April 4, 2010. Manuscript submission procedures will then be available over the Web at http://www.hipc.org. Electronic submissions must be in the form of a readable PDF file. Manuscripts must be received by May 15, 2010. Manuscripts should demonstrate current research in any area of high performance computing. All manuscripts will be reviewed and will be judged on correctness, originality, technical strength, significance, quality of presentation, and interest and relevance to the conference attendees. Submitted papers must represent original unpublished research that is not currently under review for any other conference or journal. Papers not following these guidelines will be rejected without review and further action may be taken, including (but not limited to) notifications sent to the heads of the institutions of the authors and sponsors of the conference. Submissions received after the due date, exceeding length limit, or not appropriately structured may also not be considered. Authors may contact the Program Chair at the address below for further information or clarification. Notification of review decisions will be mailed by July 17, 2010. Camera-ready papers are due by August 17, 2010. A published proceedings will be available at the conference. Program Chair: FRANCK CAPPELLO INRIA, France and Univ. of Illinois at Urbana-Champaign, USA fci at lri dot fr; cappello at illinois dot edu ----------------------------------------------------------------------------- BEST PAPER AWARDS Best paper awards, sponsored by Infosys, will be given for outstanding contributed papers. ----------------------------------------------------------------------------- WORKSHOPS Proposals are solicited for workshops to be held in conjunction with the main conference. Interested individuals should submit a proposal by May 15, 2010 to the Workshops Chair. Additional details and submission guidelines will be available at the conference website. Workshops Chair: Manimaran Govindarasu Iowa State University, USA Email: gmani at iastate dot edu ----------------------------------------------------------------------------- STUDENT RESEARCH SYMPOSIUM HiPC 2010 will feature the third student research symposium on High Performance Computing (HPC) aimed at stimulating and fostering student research, and providing an international forum to highlight student research accomplishments. The symposium will also expose students to the best practices in HPC in academia and industry. The one-day symposium will feature brief presentations by student authors on their research, followed by a poster exhibit. Short invited talks by leading HPC researchers/ practitioners will be included in the program. The symposium reception will provide an opportunity for students to interact with HPC researchers and practitioners (and recruiters) from academia and industry. To be considered, students should submit a 5 page extended abstract of their research. Submission procedures will be available at the Student Symposium web site, accessible from http://www.hipc.org, after August 17, 2010. For additional details, please see the conference web site or contact the Symposium Co-Chairs. Symposium Co-Chairs: Smruti Sarangi IBM, India Email: student_symposium at hipc dot org Ashok Srinivasan Florida State University Email: student_symposium at hipc dot org TRAVEL SCHOLARSHIPS FOR STUDENTS FROM INDIA HiPC 2010 will be awarding travel scholarships to students from Indian Engineering Colleges to encourage them to attend the conference. This merit-based scholarship will cover nominal travel and accommodation expenses. The last date of application is October 31, 2010. For more details, please visit the conference website or contact the Scholarships Co-Chairs. Scholarships Chair: Madhusudan Govindaraju SUNY Binghamton, USA Email: mgovinda at cs dot binghamton dot edu ----------------------------------------------------------------------------- ============================== HiPC 2010 ORGANIZATION ============================== GENERAL CO-CHAIRS Manish Parashar, Rutgers University, USA Rajeev Muralidhar, Intel, India VICE GENERAL CO-CHAIRS Rajendra V. Boppana, University of Texas at San Antonio, USA Rama Govindaraju, Google, USA PROGRAM CHAIR FRANCK CAPPELLO INRIA, France and Univ. of Illinois at Urbana-Champaign, USA PROGRAM VICE CHAIRS Algorithms: YVES ROBERT ENS Lyon & Institut Universtaire de France, France Architecture: TONI COSTES Barcelona Supercomputing Center, Spain Application: ESMOND G. NG Lawrence Berkeley National Laboratory USA Communication Networks: RAJEEV THAKUR Argonne National Laboratory, USA Systems software: LAXMIKANT KALE Univ. of Illinois at Urbana-Champaign, USA Mobile and sensor computing: SAJAL K DAS Univ. of Texas at Arlington and NSF, USA SUSHIL PRASAD Georgia State University, USA STEERING CHAIR Viktor K. Prasanna, University of Southern California, USA WORKSHOPS CHAIR Manimaran Govindarasu, Iowa State University, USA STUDENT RESEARCH SYMPOSIUM CO-CHAIRS Smruti Sarangi, IBM, India Ashok Srinivasan, Florida State University, USA Scholarships Chair Madhusudan Govindaraju, SUNY Binghamton, USA INDUSTRY LIAISON CHAIR Badri Ramamurthy, HP, India HiPC USER/INDUSTRY SYMPOSIUM CO-CHAIRS Srinivas Aluru, Iowa State Univ., USA, IIT Bombay, India Vipin Chaudhary, University at Buffalo, USA Naveen Sharma, Xerox, USA CYBER CHAIR Na Chen, University of Southern California, USA FINANCE CO-CHAIRS Ajay Gupta, Western Michigan University, USA Thondiyil Venugopalan, India LOCAL COORDINATION CHAIR Santhosh Daivajna, 8KMiles, India PUBLICATIONS CO-CHAIRS Sushil K. Prasad, Georgia State University, USA Raghavendra Hebbalalu, Intel, India PUBLICITY CO-CHAIRS Avinash Srinivasan, Bloomsburg University, USA Dinesh Kaushik, KAUST, Saudi Arabia Jigar Halani, Wipro, India REGISTRATION CO-CHAIRS Sally Jelinek, Electronic Design Associates, USA Jyothsna Kasturirengan, Fiberlink, India PRODUCTION CHAIR Animesh Pathak, INRIA, France STEERING COMMITTEE P. Anandan, Microsoft Research, India David A. Bader, Georgia Institute of Technology, USA Ramamurthy Badrinath, HP, India Rudramuni B., Dell India R&D, Bangalore, India Frank Baetke, HP, USA R. Govindarajan, Indian Institute of Science, India Manish Gupta, India Systems and Technology Lab, IBM, India Stefan Heinzel, Garching Computing Centre (RZG), Max Planck Society, Germany Vittal Kini, Intel, India Victor Malyshkin, Russian Academy of Sciences, Russia Ashwini K. Nanda, HPC Research Inc. Siddhartha Nandi, NetApp, India Manish Parashar, NSF and Rutgers University, USA Viktor K. Prasanna, University of Southern California, USA (Chair) Venkat Ramana, Cray-Hinditron, India Sartaj Sahni, University of Florida, USA Lokendra Shastri, Infosys, India Santosh Sreenivasan, Talentain Technologies, India V. Sridhar, Satyam Computer Services Ltd., India Harrick M. Vin, Tata Research, Development and Design Center (TRDDC), Pune, India Steering Committee 2010 membership also includes the general co-chairs, program chairs and vice general co-chairs from 2007, 2008 and 2009. ----------------------------------------------------------------------------- PROGRAM COMMITTEE Algorithms Srinivas Aluru, Iowa State University, USA Mikhail Atallah, Purdue University, USA Olivier Beaumont, INRIA & LaBRI Bordeaux, France Michael Bender, State U. New York at Stony Brook, USA Anne Benoit, ENS Lyon, France Horacio Gonzalez-Velez, Robert Gordon University, UK Phalguni Gupta, Indian Institute of Technology, Kanpur, India Phuong Hoai Ha,University of Tromso, Norway Mourad Hakem, Universit? Franche-Comt?, Belfort, France Bo Hong, Georgia Institute of Technology, USA Christos Kaklamanis, University of Patras, Greece Dariuzs Kowalski, University of Liverpool, UK Pierre Manneback, Facult? Polytechnique de Mons, Belgium Tomas Margalef, Universitat Autonoma Barcelona, Spain Padma Raghavan, Pennsylvania State University, USA Ulrich Rude, University of Erlangen Nuremberg, Germany Wolfgang Schreiner, Johannes Kepler University Linz, Austria Sandeep Sen, Indian Institute of Technology, Delhi, India Oliver Sinnen, University of Auckland, New Zealand Leonel Sousa, Technical University of Lisbon, INESC-ID, Portugal Andrew Rau-Chaplin, University of Dalhousie, Canada Jesper Larsson Traeff, Vienna University, Austria Pedro Trancoso, University of Cyprus, Cyprus Fr?d?ric Vivien, INRIA & ENS Lyon, France Fr?d?ric Wagner, IMAG Grenoble, France Application Peter Arbenz, ETH, Switzerland William Barth, Texas Advanced Computing Center, USA Johnathan Carter, Lawrence Berkeley National Laboratory, USA Edmond Chow, D.E. Shaw Research, USA Anne Elster, Norwegian University of Science& Technology, Norway Luc Giraud, INRIA, France Ananth Grama, Purdue University, USA Terence Hung, Institute of High Performance Computing, Singapore Fumihiko Ino, Osaka University, Japan Lie-Quan Lee, SLAC National Accelerator Laboratory, USA Kengo Nakajima, University of Toyko, Japan Subhash Saini, NASA Ames Research Center, USA Masha Sosonkina Ames Laboratory, USA Ashok Srinivasan, Florida State , USA Gerhard Wellein, Regional Computing Center , Germany Yao Zheng, Zhejiang University, China Communications Pavan Balaji, Argonne National Laboratory Taisuke Boku, University of Tsukuba Elisabeth Brunet, Telecom Sud Paris, France Darius Buntinas, Argonne National Laboratory Surendra Byna, NEC Laboratories America Yong Chen, Illinois Institute of Technology Rich Graham, Oak Ridge National Laboratory Torsten Hoefler, Indiana University Yutaka Ishikawa, University of Tokyo Dinesh Kaushik, King Abdullah Univ. of Sci. & Tech. and Argonne National Lab Raj Kettimuthu, Argonne National Laboratory Matt Koop, High Performance Technologies, Inc. Sameer Kumar, IBM Watson Research Center Guillaume Mercier, ENSEIRB/INRIA Raymond Namyst, University of Bordeaux -- INRIA Raju Rangaswami, Florida International University Gopal Santhanaraman, NCSA, University of Illinois Shinji Sumimoto, Fujitsu Laboratories Sayantan Sur, The Ohio State University Abhinav Vishnu, Pacific Northwest National Laboratory Weikuan Yu, Auburn University and Oak Ridge National Lab Architecture Anasua Bhowmik, AMD, India Andreas Moshovos, University of Toronto, Canada Angelos Bilas, FORTH and University of Crete, Greece Arun Sharma Google India Federico Silla, Universidad Politecnica de Valencia, Spain Georgi Gaydadjiev, Delft University of Technology, The Netherlands Mats Brorsson, Royal Institute of Technology, Sweden Meeta S. Gupta, IBM, India Parthasarathy Ranganathan, Hewlett Packard Labs, USA Pradip Bose, IBM, USA Rajeev Balasubramonian University of Utah, USA Ramon Canal, Universitat Polit?cnica de Catalunya, Spain Robert Mullins, University of Cambridge, UK Ron Brightwell, Sandia National Laboratories, USA Shubu Mukherjee, Intel, USA Smruti R. Sarangi IBM India Steve Parker, NVIDIA, USA Sudhakar Yalamanchili, Georgia Tech, USA Vassos Soteriou, Cyprus University of Technology, Cyprus Vinod Viswanath, Intel Corporation, USA Wu-chun Feng, Virginia Tech, USA Xiaoyao Liang, NVIDIA Corp. , USA Yale N. Patt, The University of Texas at Austin, USA Yoav Etsion, Barcelona Supercomputing Center Spain Mobile Elizabeth Belding-Royer, Univ California - Santa Barbara Azzedine Boukerche, Univ of Ottawa, Canada Wook Choi, Hankuk University of Foreign Studies, S. Korea Pradip De, Sentilla Inc., San Jose, USA Mario Di Francesco, Univ of Texas at Arlington, USA R. K. Ghosh, IIT Kanpur, India Ahmed Helmy, Univ of Florida, USA Bhaskar Krishnamachari, Univ of Southern California, USA Cristina Pinotti, Univ of Perugia, Italy Sushil Prasad, Georgia State Univ, USA Behrooz Shirazi, Washington State Univ, USA Wade Trappe, WINLAB, Rutgers Univ, New Jersey, USA Yuanyuan Yang, Stony Brook University, USA Albert Zomaya, Univ of Sydney, Australia System software Sanjeev Aggarwal, Indian Institute of Technology, India Eduard Ayguade, UPC and Barcelona Supercomputing Center, Spain Henri Bal, Vrije Universiteit, Netherlands Rajkumar Buyya, University of Melbourne, Australia Rudolf Eigenmann, Purdue University, USA R Govindarajan, Indian Institute of Science, India Attila Gursoy, Koc University, Turkey Uday Khdekar, Indian Institute of Technology, Bombay, India Orion Sky Lawlor, University of Alaska, USA Philippe O. A. Navaux, UFRGS, Brazil Pradeep Padala, DOCOMO Labs, USA Depei Qian China, Beihang University Mitsuhisa Sato, University of Tsukuba, Japan Stephen L. Scott, ORNL, USA Sameer Shende, University of Oregon, USA Allan Sussman, University of Maryland, USA Sathish Vadhiyar, Indian Institute of Science, India Richard Vuduc, Georgia Institute of Technology, USA GuangWen Yang, Tsinghua University, China -- Jigar Halani Publicity co-chair - HiPC www.hipc.org Please do not print this email unless it is absolutely necessary. The information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. WARNING: Computer viruses can be transmitted via email. The recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. www.wipro.com From neuro.informatics.at.mbl at gmail.com Mon Mar 15 19:19:31 2010 From: neuro.informatics.at.mbl at gmail.com (Neuro Informatics) Date: Mon, 15 Mar 2010 19:19:31 -0400 Subject: [BiO BB] Announcement: Neuroinformatics course at Marine Biological Laboratory, Woods Hole, MA, August 14-29, 2010 Message-ID: <45f3a6f11003151619m7dbc62bcuac21a812b092c521@mail.gmail.com> Neuroinformatics course at Marine Biological Laboratory, Woods Hole, MA Dates: August 14th to 29th, 2010 Web: http://www.mbl.edu/education/courses/special_topics/neufo.html The objective of this two week course is to develop an understanding of the methods of managing and analyzing data sets from neurophysiological and behavioral measurements, particularly large data volumes that require systematic statistical and computational approaches. The course includes lectures on fundamental analytical methods, established and emerging applications and focused hands-on computer-based sessions. Topics include point processes (*e.g., *spike trains), continuous processes (*e.g.*, LFP/ECoG/EEG/MEG recordings, fMRI, and behavioral recordings), and methods for analyzing neuroanatomical (*e.g., *light and electron microscopy) data. Various statistical techniques for exploratory and confirmatory analysis of the data will be treated along with underlying scientific questions and potential applications. The course also includes tutorials on computer methods and discussions of major open issues in the field. The course is targeted broadly, from experimental researchers to researchers with a theoretical or analytical orientation who work closely with data. A main aim of the course is to foster close working relations between the theorists and experimentalists. Researchers at all levels, from advanced graduate student to working professional, may benefit from the course. Application deadline is April 16, 2010. Limited to 26 participants. Computer Laboratory: A hands-on approach will be taken in a computer laboratory that forms an integral part of this course. Example data sets will be supplied, and participants are encouraged to bring their own data. We will primarily use MATLAB, with additional tools used as needed (*e.g.*, MySQL). Participants will be guided in applying analytical techniques to the example data sets and will further participate in a structured "data analysis challenge", in which teams will analyze published data sets in the context of specific questions. This should benefit both experimental researchers that wish to analyze their own data sets and theorists who want to work with data. Structure of the Course: The first week will contain lectures dealing with fundamental statistical and analytical techniques appropriate for neural data analysis. A concurrent computer laboratory will run in the evenings to supplement the lectures. The second week contains application-based lectures, focused on emerging research areas and associated analytical and experimental techniques, along with the "data analysis challenge". From dan.bolser at gmail.com Thu Mar 18 19:05:18 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 18 Mar 2010 23:05:18 +0000 Subject: [BiO BB] Fwd: [Bioperl-l] Google Summer of Code is *ON* for OBF projects! In-Reply-To: <4BA29706.8040606@cornell.edu> References: <4BA29706.8040606@cornell.edu> Message-ID: <2c8757af1003181605y30ed80cla6d7ec34472985b8@mail.gmail.com> ---------- Forwarded message ---------- From: Robert Buels Date: 18 March 2010 21:11 Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects! To: Hi all, Great news: Google announced today that the Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer's Google Summer of Code! GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). ? Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see GSoC 2010 FAQ at http://tinyurl.com/yzemdfo Student applications are due April 9, 2010 at 19:00 UTC. ?Students who are interested in participating should look at the OBF's GSoC page at http://open-bio.org/wiki/Google_Summer_of_Code, which lists project ideas, and who to contact about applying. For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project's GSoC wiki page. Thanks to all who helped make OBF's application to GSoC a success, and let's have a great, productive summer of code! Rob Buels OBF GSoC 2010 Administrator _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From isbra-l at engr.uconn.edu Tue Mar 23 17:54:48 2010 From: isbra-l at engr.uconn.edu (ISBRA Symposium Announcements) Date: Tue, 23 Mar 2010 17:54:48 -0400 Subject: [BiO BB] [ISBRA-L] WABI'10 Call for Papers In-Reply-To: References: Message-ID: Dear Colleague: We are pleased to announce the call for papers for WABI'10, the 10th Workshop for Algorithms in Bioinformatics. WABI will be part of ALGO 2010, and will be hosted by the University of Liverpool, UK. The conference will run from Sept 6 to 10, 2010, and the submission deadline is May 7, 2010. We welcome papers on algorithmic work in bioinformatics, computational biology and systems biology. Please see our website for details. http://algo2010.csc.liv.ac.uk/wabi Thank you, Vincent Moulton Mona Singh WABI Program Chairs _______________________________________________ ISBRA-L mailing list To change subscription options visit http://dna.engr.uconn.edu/mailman/listinfo/isbra-l From hlapp at gmx.net Fri Mar 26 15:59:24 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 26 Mar 2010 15:59:24 -0400 Subject: [BiO BB] Phyloinformatics Summer of Code 2009 - Call for student applications Message-ID: *** Please disseminate widely at your local institutions, including *** *** posting to message and job boards, so that we reach as many *** *** students as possible. *** PHYLOINFORMATICS SUMMER OF CODE 2010 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2010 The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/ ). Students in the program will receive a stipend from Google (and possibly more importantly, a T-shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. NESCent is particularly targeting students interested in both evolutionary biology and software development. Initial project ideas are listed on the website. These range from phylogenetics pipeline development to a user interface for MIAPA-driven annotation of experiments, interactive animations of gene tree evolution, and rendering phylogenies on Google Earth. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/ ), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students opens on Monday March 29th and runs through Friday, April 9th, 2010. INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. 2010 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2010 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2010/faqs DataONE Summer 2010 Internship Program (managed separately, and different from GSoC; postdocs also eligible): http://d1-lab.appspot.com/ --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org From hlapp at gmx.net Sat Mar 27 14:12:31 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 27 Mar 2010 14:12:31 -0400 Subject: [BiO BB] Phyloinformatics Summer of Code 2010 - Call for student applications In-Reply-To: References: Message-ID: <52BE7CDC-1D5D-4E53-B82D-D3CF30303750@gmx.net> Typo alert: On Mar 26, 2010, at 3:59 PM, Hilmar Lapp wrote: > 2010 NESCent Phyloinformatics Summer of Code: > http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2010 The hostname is wrong in this URL. The correct URL is the one given at the top of the original email: http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2010 -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From dan.bolser at gmail.com Mon Mar 29 04:48:43 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 29 Mar 2010 09:48:43 +0100 Subject: [BiO BB] Announcing OBF Summer of Code Message-ID: <2c8757af1003290148o78636383kaa8a03af783a099f@mail.gmail.com> OPEN BIOINFORMATICS FOUNDATION SUMMER OF CODE 2010 Applications due 19:00 UTC, April 9, 2010. http://www.open-bio.org/wiki/Google_Summer_of_Code The Open Bioinformatics Foundation Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for bioinformatics under the mentorship of experienced developers from around the world. The program is the participation of the Open Bioinformatics Foundation (OBF) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/). Students successfully completing the 3 month program receive a $5,000 USD stipend, and may work entirely from their home or home institution. ?Participation is open to students from any country in the world except countries subject to US trade restrictions. ?Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. The Open Bioinformatics Foundation is particularly seeking students interested in both bioinformatics (computational biology) and software development. Some initial project ideas are listed on the website. These range from Galaxy phylogenetics pipeline development in Biopython to lightweight sequence objects and lazy parsing in BioPerl, a DAS Server for large files on local filesystems, and mapping Java libraries to Perl/Ruby/Python using Biolib+SWIG+JNI. ?All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome and encourage students proposing their own project ideas; historically some of the most successful Summer of Code projects are ones proposed by the students themselves. TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students runs from Monday, March 29 through Friday, April 9th, 2010. INQUIRIES: We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. ?See the OBF GSoC page for contact details. 2010 OBF Summer of Code: http://www.open-bio.org/wiki/Google_Summer_of_Code Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2010/faqs