From julianthomasp from gmail.com Tue Jan 1 11:18:36 2008 From: julianthomasp from gmail.com (j_thomas) Date: Tue Jan 1 12:01:17 2008 Subject: [Computational-biology] Lecture on Protein Ligand Modelling Message-ID: Lecture on Protein Ligand Modelling http://bioisolutions.blogspot.com/2007/12/protein-ligand-modelling.html or http://tinyurl.com/227kty -- Sincerely, Julian Thomas http://bioisolutions.blogspot.com/ From rpwise from iastate.edu Fri Jan 4 18:37:24 2008 From: rpwise from iastate.edu (Roger Wise) Date: Fri Jan 4 20:26:13 2008 Subject: [Computational-biology] Postdoctoral Position - Bioinformatics Message-ID: Postdoctoral Position - Bioinformatics/Computational Biology USDA-ARS / Iowa State University Functional Genomics of Plant Disease Defense A postdoctoral research position is available immediately in the Crop Genomics and Informatics Laboratory (CGIL), a collaborative effort of ARS and Iowa State University scientists. The overall goals of the "Functional Genomics of Plant Disease Defense" project are to utilize genomics tools and resources to accelerate comparative analysis of disease defense pathways important in agriculture (http://nsf.gov/awardsearch/showAward.do?AwardNumber=0500461). The candidate will work with a team responsible for molecular, genetic, and functional characterization of genes associated with and required for R-gene mediated resistance responses using barley powdery mildew and barley stem rust as model systems. The candidate will work with GeneNetwork [http://www.genenetwork.org/] to integrate eQTL analysis modules into the multi-crop plant expression database, PLEXdb [http://plexdb.org/] to enable visualization and analysis of quantitative gene expression- and trait data collected from segregating populations and diversity panels. Biologically relevant co-expression networks will be extracted and tested for function in disease defense. Recent Ph.D. in Bioinformatics/Computational Biology or a closely related field is required. Knowledge of Genetics/Cell Biology/Pathology/Biochemistry are desirable. Salary starts at $54,494 (GS-11). Funding is available for two years with possibility of extension. INFORMATION ON SALARY AND APPLICATION PROCEDURES is available at: http://www.afm.ars.usda.gov/divisions/hrd/hrdhomepage/vacancy/pd962.html Citizenship limitations may apply; see http://www.afm.ars.usda.gov/hrd/jobs/VISA/countries.htm INFO ON EMPLOYEE BENEFITS is available at: http://www.usajobs.opm.gov/ei61.asp Highly motivated individuals should send curriculum vitae, research interests, and reprints to the address below (Include name, e-mail, address, phone, and fax no. of three references) Dr. Roger Wise, USDA-ARS Department of Plant Pathology 351 Bessey Hall Iowa State University, Ames, IA 50011-1020 USA Phone: 515-294-9756 Fax: 515-294-9420 E-mail: rpwise@iastate.edu http://wiselab.org/ http://plexdb.org/ http://barleygenome.org/ Refer to Announcement No. RA-07-016H From prash from ruc.dk Mon Jan 7 06:27:26 2008 From: prash from ruc.dk (Prash) Date: Mon Jan 7 10:02:21 2008 Subject: [Computational-biology] Call :'Systems Biology in present day Bioinformatics' Message-ID: <1199705246.47820c9e3dfed@webmail.ruc.dk> Dear All, As a session organizer of the following conference, I would like to invite you all for your participation in Florida http://www.infocybereng.org/imeti2008/Invitedsession/ISOrganization.asp?vc=6 The detailed information on participation follows my signature: Best, prash ----- Forwarded message from citsa2008@mail.infocybereng.org ----- Date: Fri, 4 Jan 2008 19:46:44 -0400 From: citsa2008@mail.infocybereng.org Reply-To: citsa2008@mail.infocybereng.org Subject: CITSA 2008 Invited Session Acceptation To: prash@ruc.dk Dear Prashanth Suravajhala: Thank you for submitting your proposal for organizing an invited session titled: 'Systems Biology in present day Bioinformatics'. It is our pleasure to inform you that the title of the invited session you proposed has been accepted, i.e. the invited session was pre-approved. As soon as you collect, review and approve at least 5 papers to be presented in your session, we will process your invited session proposal for its definitive approval and its inclusion in the Conference Program. Since you will be organizing the session, you will also chair it, or you can appoint its chair. We would like to inform you that organizers of invited sessions with the best performance will be co-editors of the proceedings volume where their session's papers were included, and co-editors of the electronic proceedings in CD.They will also be candidates for invited editors, or co-editors, of a possible JSCI journal issue with a special area related to the topic of their invited session's papers. Furthermore, they will chair their respective invited session and will be asked to choose the best paper of it.The best 30% of all (invited and regular) sessions' best papers will be published in the JSCI Journal. This journal is published in electronic and hard copy versions. The hard copy version is being sent, via complimentary subscriptions for 2 years, to 200 universities' and research organizations' libraries.The organizations of the authors publishing in the JSCI are the candidates with the first priority to receive complimentary subscriptions of all the journal's issues for the next 2 or 3 years. We are pleased to send you the following information related to the organizing process of an invited session, where you have already covered the first 3 steps: 1) Identify a special topic in the scope of CITSA 2008, and the invited session title 2) Fill the invited session organization form, provided in the conference web page http://infocybereng.org/CITSA2008/organizer.asp If for any reason you are not able to access the page mentioned above, please, try the following page: http://infocybereng.org/CITSA2008/default.asp. If you don?t have access to the web, please, contact the CITSA 2008 Secretariat to the following e-mail: citsa2008@mail.infocybereng.org. 3) If the identified topic is suitable, the General Chair will accept the proposal, and you will receive an acceptation by e-mail, in a few days. This acceptation is not a final approval of the proposed session, but a pre-approval. The final approval will depend on identifying at least five papers for the proposed session, to be presented at the conference, and informing, at least, about their titles. With this acceptation: a) the proposed session will be included in the conference web page as well as its organizer?s and chair?s names, and b) its organizer will be able to announce his/her invited session in the context of CITSA 2008, by any media that he/she thinks appropriate, such as: Web page, hard-copy call for papers, call for papers attached to e-mails, etc. The invited session organizer has the responsibility of his or her session content. 4) Contact researchers and/or practitioners in your field to see if they can contribute a paper to your proposed session and attend CITSA 2008. 5) Collect the extended abstracts or the paper drafts from each prospective participant. 6) As soon as you have 5 reviewed and accepted papers, you will complete the form regarding the invited session papers, provided in the conference web page http://infocybereng.org/CITSA2008/organizer.asp . 7) Step 6 will take your invited session to the status of an approved one if the papers fulfill all the requirements (i.e. quality). All the approved invited sessions will be included in the CITSA 2008 Conference Program. 8) No author, including the organizer, can present more than two papers in the invited session. A scholar/researcher can co-author more papers, but he, or she, cannot present more than two papers in the same invited session. We would like to take this opportunity to inform you about the role of invited session organizers. An invited session organizer has a similar role to the invited editor in a journal, i.e. he or she is invited to identify and look for high quality papers, to review the papers of his, or her, session, to select the reviewers that will help him, or her, and to decide which papers he/she wants to be presented at the respective invited session. The invitation is an academic, not a financial one, because, unfortunately, we have no financial sponsor and the conference should self-finance itself. Consequently, we cannot make any financial commitment. In this way we are trying to give a first step in re-engineering the process of organizing a conference: to move decisions to the right people, to those interfacing with the conference users, for example, the authors. Our experience in the last 10 events we organized showed us that the invited organizers help a lot into achieving higher quality levels. So, an invited session organizer can dedicate his/her time and efforts to improve the papers quality in the research area of his/her interest and CITSA 2008 Organizing Committee will provide him/her with the place, the logistics, the proceedings, the intellectual and the physical context, etc. All that the invited session organizer has to worry about is the quality of the papers to be presented in her/his session(s). Every session organizer will chair his/her session(s), and will be a member of CITSA 2008 Program Committee and might be one of the co-editors of one volume of the hard copy and the CD version of the proceedings, if his/her session(s) is(are) among the largest invited session(s) published in the respective volume. Depending on the quality and quantity of the papers of his/her session(s), as well as on the scope of the possible interested audience, IIIS may ask him/her, to edit, or co-edit, a multiple authors book to be published. An invited Session Organizer is in charge of the reviewing process of her/his invited session papers (directly and/or by means of a Focal Program Committee she/he selects for her/his session), and she/he can make her/his own timetable, as long as the camera-ready papers are ready by the respective deadline, and she/he informs us about the initial set of accepted papers (at least 5 titles and their respective authors and e-mails) by the announced respective deadline. The invited session organizer has the autonomy required as to be the responsible regarding the quality of the papers to be presented in his, or her, session. The Invited Session organizer will chair his/her session. While chairing it, she/he will determine oral presentation time according to the number of participants physically present. Usually 2-2:30 hours are allocated for each session containing an average of 5 papers, with a maximum of 6. Sometimes we include 7 papers in a session because statistically 10-15% of the registered persons don't show up. Then, when we allocate 7 papers, we are expecting a maximum of 6 oral presentations. When an Invited Session has more than 7 papers with their respective 7 registered participants, we allocate them into two time blocks of 2-2:30 hours for each block. When an Invited Session has more than 14 papers (and their respective registered participants), we allocate the presentation in three time blocks of 2-2:30 hours each block, and soon. An invited session organizer can organize and chair several invited sessions in the same topic and with the same title, or she/he can organize several sessions in different topics and with different titles. If an Invited Session Organizer has an unforeseen hindrance in the last moment, and cannot be physically present in the conference, she/he will advice us about the author (of the session) that can chair for her/him session, and the invited session organizer can still be a co-editor of the proceedings and/or be selected to co-edit a multiple authors book based fundamentally on the papers of her/his session, as long as the requirements given above are fulfilled. Prashanth Suravajhala PhD Fellow http://ruc.dk/~prash/ The important thing is not to stop questioning. 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<3feaadfe-ff3e-4a6e-a6d7-7a49fce11c8d@c4g2000hsg.googlegroups.com> Extended Search DIRECTOR OF BIOINFORMATICS Roy J. Carver Biotechnology Center University of Illinois at Urbana-Champaign Proposed Starting Date: As soon as possible, after closing Qualifications: Ph.D. in Bioinformatics or in a field related to Life Sciences with experience in bioinformatics. Expertise is required in all aspects of bioinformatics processing of genomic, EST, and metagenomic DNA sequencing approaches including traditional Sanger, as well as new emerging sequencing technologies. This position also requires excellent communication skills, understanding of computer hardware and software, and the ability to work both independently and as part of a team. Candidates must be eligible to work in the U.S. Responsibilities: The University of Illinois Carver Biotechnology Center is a core user facility that assists campus researchers in genomic, proteomic, and metabolomic experimentation. Responsibilities of this position are to direct the staff of the Bioinformatics Unit of the Carver Biotechnology Center, to manage and enhance the resources of the Center, and to guide projects initiated within the University and by external researchers. The successful candidate will work closely with faculty and staff in bioinformatics processing of research projects. Director will actively work on and manage processing, assembly, and annotation of DNA sequencing, archiving data, maintenance of in-house developed software, data mining, and to carry out and advise on microarray data analysis. In addition, the Carver Biotechnology Center sponsors workshops in genomics and proteomics in which the Director of Bioinformatics will assist. Type of Position: Full-time Academic Professional. Salary is commensurate with experience. Application: Submit cover letter, resume, academic transcript(s), and at least 3 letters of reference to: Rhonda Lipking, Administrative Secretary Roy J. Carver Biotechnology Center, 2613 Institute for Genomic Biology 1206 W. Gregory Drive, Urbana, IL 61801 Phone: (217) 333-1695, Email: lipking@uiuc.edu For additional information: Dr. Mark Mikel, Associate Director, Roy J. Carver Biotechnology Center; Phone: (217) 244-0144; Email: mmikel@uiuc.edu Deadline: For full consideration, applications must be received by 5:00 pm, February 15, 2008. The University of Illinois is an affirmative action/equal opportunity employer From HISHAM from uhcl.edu Wed Jan 9 10:58:33 2008 From: HISHAM from uhcl.edu (Al-Mubaid, Hisham) Date: Wed Jan 9 13:15:45 2008 Subject: [Computational-biology] SEDE-2008 (USA) CFP: Submission Deadline: February 22, 2008 Message-ID: <4B57CB6706E6144C9D5D960FEEDA8E8E013EC6DD@EXUHCL1.pclab.uhcl.edu> Apologies for receiving multiple copies: Deadline for paper submission: February 22, 2008 CALL FOR PAPERS SEDE-2008 17th International Conference on Software Engineering and Data Engineering June 30 - July 2, 2008, Los Angeles, California USA Sponsored by the International Society for Computers and Their Applications (ISCA) Conference Website: http://sce.cl.uh.edu/sede08/ The 17th SEDE Conference seeks high quality submissions in all areas of Software Engineering (SE) and Data Engineering (DE). This year the conference puts special emphasis on the impact of ubiquitous and pervasive computing on software engineering and data engineering. Applied case studies will report on exemplary solutions deployed in industries like aerospace, telecommunications and military. In the SE section particular emphasis will be placed on techniques for software specification and design of software/hardware components and the modeling of system architectures. In the DE section, the emphasis this year is on high performance algorithms that learn patterns from large volumes of data, learn and predict events, adapt to situations, rationalize, provide autonomous control, and assist in executive decision-making. The conference also includes a BEST PAPER AWARD given for a paper presented at the conference. The conference will cover a broad range of topics including, but not limited to, the following topics. Software Engineering Software Modeling, Development, & Maintenance Software Requirements Engineering Software Verification and Model Checking Reengineering and Reverse Engineering AI and Knowledge Based Software Engineering Agent-Oriented Software Engineering Formal and Semiformal Methods Object-Oriented and Model-Driven Techniques Service- and Aspect-Oriented Techniques Web Engineering and Agents Programming and Description Languages Software Visualization and Program Understanding Software Quality and Software Metrics Software Security, Safety, Reliability Software Components & Software Architectures Process, Project Management Human Computer Interaction Internet and Information Systems Development Software Engineering Education Applications and Case Studies Data Engineering Distributed, Parallel, and Peer to Peer Database Semi-structured Data and XML Database Data Integration, Interoperability, and Metadata Data Mining: Traditional, Large-scale, Parallel Data Mining Ubiquitous Data Management and Mobile Database Data Privacy and Security Scientific and Biological Databases and Bioinformatics Data Grids, Data Warehousing, OLAP Temporal, Spatial, Sensor, and Multimedia Database Taxonomy and Categorization Pattern Recognition, Clustering, and Software Classification Knowledge Management and Ontologies Query Processing, Query Optimization, and Data Structures Database Applications and Experiences Web Data Management and Deep Web INSTRUCTIONS TO AUTHORS Papers will be accepted ONLY BY ELECTRONIC SUBMISSION in PDF format. Include a cover page containing title, author's name(s), address, affiliation, email address, telephone number and topic area. In cases of multiple authors, all correspondence will be sent to the first author unless otherwise requested. Authors must submit a full paper (no more than 15 double spaced pages) by FEBRUARY 22, 2008. All submissions must be uploaded through the conference web page Click Here . If you encounter any difficulties during submission or if you require further information, please contact: isca@ipass.net. The submitted manuscript should closely reflect the final paper as it will appear in the proceedings, which will be a maximum of 6 pages (+2 pages with additional page fees) in ISCA format. (See http://www.isca-hq.org/sample-isca-manuscript-format.pdf) Program Co-Chair: Program Co-Chair: Rym Zalila Mili Hisham Al-Mubaid University of Texas at Dallas University of Houston - Clear Lake Voice: +1 (972 ) 883-2091 Voice: +1 (281) 283-3802 E-mail: rmili@utdallas.edu E-mail: hisham@uhcl.edu IMPORTANT DATES Deadline for paper submission: February 22, 2008 Notification of acceptance: April 25, 2008 Camera ready papers due: May 16, 2008 __________________________________________________________________________________________________________ CONFERENCE CHAIR: Narayan Debnath Winona State U., USA E-mail: ndebnath@winona.edu PROGRAM CO-CHAIRS: Rym Zalila Mili, U. of Texas-Dallas, USA Hisham Al-Mubaid, U. of Houston-Clear Lake, USA INTERNATIONAL PROGRAM COMMITTEE: Sultan Aljahdali, Taif U., Saudi Arabia Khalid Buragga, King Faisal U., Saudi Arabia Mark Burgin, UCLA, USA Maurice Cohen, U. of California, USA Kendra Cooper, U. of Texas at Arlington, USA Alfredo Cuzzocrea, U. of Calabria, Italy Sergiu Dascalu, U. of Nevada, Reno Wei Ding, U. of Houston-Clear Lake, USA Sherif Elfayoumy, U. of North Florida, USA Adel Elmaghraby, U. of Louisville, USA Edgar Gabriel, U. of Houston, USA Hisham Haddad, Kennesaw State U, USA Ramzi Haraty, Lebanese American U., Lebanon Frederick Harris, UNR, USA Ehab Hassanein, Cairo U., Egypt Gongzhu Hu, Central Michigan U., USA Ahmed Kamel, Concordia College, USA Tatjana Kapus, U. of Maribor, Slovenia David King, U. of Texas at Arlington, USA Dieter Kranzm?ller, U. of Linz, Austria Cyril S. Ku, William Paterson U., USA Gordon Lee, San Diego State U., USA Jeff Lei, U. of Texas at Arlington, USA P. K. Mahanti, U. of New Brunswick, Canada Eda Marchetti, U. of Pisa, Italy Pornsiri Muenchaisri, Chulalongkorn U., Thailand Mara Nikolaidou, U. of Athens, Greece David Pheanis, Arizona State U., USA Imad Rahal, College of St Benedict|St. John's U., USA Venkat Subramanian, U. of Houston, USA Fu-Shing Sun, Ball State Univ, USA Jeff Tian, Southern Methodist U., USA Elizabeth Wang, Waynesburg U., USA Eric Wong, U. of Texas at Dallas, USA W. Lok Yeung, Lingnan U., Hong Kong Kwok-Bun Yue, U. of Houston-Clear Lake, USA Qinghua Zou, Microsoft Research, USA __________________________________________________________________________________________________________ Questions? Contact Mary Ann Sullivan at: ISCA@ipass.net h2 From prash from ruc.dk Tue Jan 8 11:51:09 2008 From: prash from ruc.dk (Prash) Date: Wed Jan 9 13:23:50 2008 Subject: [Computational-biology] Several Post Doc/PhD positions in Computational/Systems Biology Message-ID: <1199811069.4783a9fd88183@webmail.ruc.dk> http://www.nature.com/naturejobs/science/jobs/36679 http://www.nature.com/naturejobs/science/jobs/38231 http://www.nature.com/naturejobs/science/jobs/39005 http://www.nature.com/naturejobs/science/jobs/39012 http://www.nature.com/naturejobs/science/jobs/39038 http://www.nature.com/naturejobs/science/jobs/38941 http://www.nature.com/naturejobs/science/jobs/38950 http://www.nature.com/naturejobs/science/jobs/38040 http://www.nature.com/naturejobs/science/jobs/38441 http://www.nature.com/naturejobs/science/jobs/35589 http://www.nature.com/naturejobs/science/jobs/34730 http://www.embo.org/yip/positions.php http://www.nature.com/naturejobs/science/jobs/38950 http://www.nature.com/naturejobs/science/jobs/35855 http://www.nature.com/naturejobs/science/jobs/37746 http://www.nature.com/naturejobs/science/jobs/35768 http://www.nature.com/naturejobs/science/jobs/36830 http://www.nature.com/naturejobs/science/jobs/37284 http://www.nature.com/naturejobs/science/jobs/36830 http://www.nature.com/naturejobs/science/jobs/36845 http://www.nature.com/naturejobs/science/jobs/35589 Best, Prash Prashanth Suravajhala PhD Fellow http://ruc.dk/~prash/ The important thing is not to stop questioning. Curiosity has its own reason for existing ~Albert Einstein From prash from ruc.dk Wed Jan 9 09:29:38 2008 From: prash from ruc.dk (Prash) Date: Wed Jan 9 13:24:02 2008 Subject: [Computational-biology] ISMB08 CFP, C-SHALS/AMIA/MCBIOS Calls For Registration, ISCB Software Policy Statement, ECCB08 CFP Message-ID: <1199888978.4784da525e605@webmail.ruc.dk> :: ISCB ANNOUNCEMENTS AND U P D A T E S :: ISMB 2008, July 19-23, Toronto, Canada Call for Papers Closing in One Week www.iscb.org/ismb2008/sub_papers.php Paper Submission Deadline: January 16, 2008 _________________________ C-SHALS 2008, March 5-7, Boston/Cambridge, MA, USA 1st Annual ISCB Conference on Semantics in Healthcare & Life Sciences - Registration Now Open www.iscb.org/cshals2008/ Keynotes and session speakers will be added to the website within days for your immediate information. _________________________ AMIA Summit on Translational Bioinformatics, March 10-12, San Francisco, USA (an ISCB Affiliated Conference) Final days for early bird registration savings www.amia.org/meetings/stb08/index.asp Early registration deadline: January 11, 2008 ISCB member savings as high as $200 USD _________________________ MCBIOS 5th Annual Conf on MidSouth Computational Biology & Bioinformatics Society (an ISCB Affiliated Regional Group), February 23-24, Oklahoma City, USA Early registration and poster abstracts closing soon www.mcbios.org Early registration deadline: January 11, 2008 Poster abstract submission deadline: February 1, 2008 _________________________ ISCB Policy Statement on Bioinformatics Software Availability Request for Comment on Current Statement for Possible Revision http://iscb-discussion.blogspot.com/2007/06/data-and-software-sharing-po licy.html Comments Deadline: January 31, 2008 _________________________ ECCB 2008, September 22-26, Cagliari, Sardinia, Italy (an ISCB Affiliated Conference) Mark your calendar now to prepare for upcoming submission dates www.eccb08.org/index.php?pageId=1 Paper Submission Deadline: February 11, 2008 _________________________ ISCB Membership - Join or Renew Now www.iscb.org/membership Courtesy: Dr. BJ Morrison Prashanth Suravajhala PhD Fellow http://ruc.dk/~prash/ The important thing is not to stop questioning. 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OyZuYnNwO0FzIHRoZSBtYWlsaW5nIGxpc3QgaXMgdXBkYXRlZCB3ZWVrbHksIHlvdSB3aW xsIGJl IHVuc3Vic2NyaWJlZCB3aXRoaW4gc2V2ZW4gZGF5cy48L0ZPTlQ+PC9TUEFOPjwvUD4NCj xCUj4N Cg0KPC9CT0RZPg0KPC9IVE1MPg== From rhorler from life.uiuc.edu Wed Jan 9 17:26:59 2008 From: rhorler from life.uiuc.edu (Richard Horler) Date: Wed Jan 9 23:51:05 2008 Subject: [Computational-biology] Nucleotide Pairing Message-ID: <47854A33.1050802@life.uiuc.edu> Hi I was wondering if anyone knows of a software which would allow me to compare sequences to look for the maximum RNA:RNA base pairing. i.e. if I input two RNA sequences the program could run through all possible alignments and determine which is most stable i.e. most cognate base pairs preferably including the none standard Watson Crick base pairs. Richard From darek.kedra from gmail.com Thu Jan 10 19:55:34 2008 From: darek.kedra from gmail.com (darked) Date: Fri Jan 11 12:58:49 2008 Subject: [Computational-biology] Re: Nucleotide Pairing References: Message-ID: <5dcfdb84-6e72-4c22-be64-e28b654e051b@d21g2000prf.googlegroups.com> Richard Horler wrote: > Hi > > I was wondering if anyone knows of a software which would allow me to > compare sequences to look for the maximum RNA:RNA base pairing. i.e. if > I input two RNA sequences the program could run through all possible > alignments and determine which is most stable i.e. most cognate base > pairs preferably including the none standard Watson Crick base pairs. > > Richard I am not sure if this will answer your questionn but you may try as starting point: http://openwetware.org/wiki/Wikiomics:RNA_homology_search and RNAhybrid: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/ Best, Darek Kedra http://openwetware.org/wiki/Wikiomics From darek.kedra from gmail.com Mon Jan 14 08:49:10 2008 From: darek.kedra from gmail.com (darked) Date: Mon Jan 14 12:56:04 2008 Subject: [Computational-biology] Re: Nucleotide Pairing References: Message-ID: <2afb385a-9be6-4c59-8773-2648260d69f0@v67g2000hse.googlegroups.com> On Jan 9, 10:26 pm, Richard Horler wrote: > Hi > > I was wondering if anyone knows of a software which would allow me to > compare sequences to look for the maximum RNA:RNA base pairing. i.e. if > I input two RNA sequences the program could run through all possible > alignments and determine which is most stable i.e. most cognate base > pairs preferably including the none standard Watson Crick base pairs. > > Richard Something has eaten me previous answer.. Well, you can try http://foldalign.ku.dk/ You will find more programs here: http://openwetware.org/wiki/Wikiomics:RNA_secondary_structure_prediction Best, Darek Kedra http://openwetware.org/wiki/Wikiomics From nicola.cannata from unicam.it Wed Jan 16 16:19:52 2008 From: nicola.cannata from unicam.it (Nicola Cannata) Date: Wed Jan 16 16:50:47 2008 Subject: [Computational-biology] CALL FOR PAPERS: FBTC 2008 Message-ID: ************************************************************************* Call For Papers ************************************************************************* Second International Workshop From Biology To Concurrency and back (FBTC 2008) A Satellite Workshop of ICALP 2008 July 12, 2008, Reykjavik, Iceland http://www.cs.le.ac.uk/events/FBTC2008 ************************************************************************* SUMMARY: In computational theory, several formal approaches make use of biology as inspiration for the development of problem solving techniques. Most of them are taken from complex, inherently concurrent, systems. Some examples of "biologically inspired computing" are artificial immune systems, cellular automata, genetic algorithms, membrane computing, neural networks, organic computing, swarm intelligence. On the other hand, concurrency has begun to inspire an emerging research area in Biology. Regev and Shapiro coined the Cells-as-Computation metaphor as the "much-needed abstraction for biomolecular systems". Computers and biomolecular systems both start from a small set of elementary components from which, layer by layer, more complex entities are constructed with evermore sophisticated functions. In computational systems biology, the abstractions, tools and methods used to specify and study concurrent and distributed systems can therefore be naturally adopted to model and better understand the complex biomolecular systems. In this workshop we intend to explore this "cross-fertilization" between computational sciences and biology, with a special attention to concurrent models in biology and formal foundations in bio-inspired computing. Concurrency theory permits hypotheses generation and testing. Models can therefore be simulated, analyzed, checked and validated. A growing "arsenal" of theoretical models, logics, and tools for understanding concurrent systems has been developed. We recognize that concurrency permeates not only computer systems but also nature and living organisms. We can find concurrency at the molecular level as well as at those of cells, organs, individuals, communities and ecological systems. Also, biologically inspired computing could benefit from concurrency theory. SPECIFIC TOPICS OF INTEREST INCLUDE (BUT ARE NOT LIMITED TO): * Biologically inspired developments in concurrency theory; * Biologically inspired models and software tools for concurrent computation; * Applications of computer science formalisms with concurrency flavour, such as process algebras, Petri nets, automata, statecharts, rewrite systems, P systems, in systems biology; * Challenges in compositional modelling of biological systems at different level of detail: molecular, cellular, tissue, organs, organism, community; * Use of concurrency software tools in the modelling, simulation and analysis of biological systems. PAPER SUBMISSION: We solicit unpublished papers reporting on original research on the topics of interest of FBTC workshops. The title and the abstract of each paper should be sent to the email address of the workshop by Wednesday 12 of March, 2008 and papers should be submitted via EasyChair (http://www.easychair.org/conferences/?conf=fbtc2008) by Wednesday 19 of March 2008. Authors will be notified of acceptance by Friday, 2 May 2008. Submissions from the PC members are allowed. Prospective authors may need to register with EasyChair first if they do not have an account there yet. Papers should take the form of a pdf file in ENTCS format, whose length should not exceed 15 pages. Please follow the instructions at http://www.entcs.org/prelim.html for downloading the correct prentcsmacro.sty file for FBTC 2008. If necessary, detailed proofs of technical results and other additional information can be included in a clearly-labelled "Appendix for referees". This is in addition to 15 pages stated above; and the material may be read at the discretion of the PC but will be included in the final version of the paper. Submissions from the PC members are allowed. Proceedings: Bound preliminary proceedings will be available at the meeting. The final proceedings of the workshop will appear as a volume in the ENTCS series. IMPORTANT DATES: * Submission of title and abstract: 12 March 2008 * Submission of paper: 19 March 2008 * Notification: 2 May 2008 * Final version: 23 May 2008 * Workshop: Saturday, 12 July 2008 * Final ENTCS version: 22 August 2008 PROGRAMME COMMITTEE: Uwe Aickelin (University of Nottingham, UK) Ezio Bartocci (University of Camerino, IT) Chiara Bodei (University of Pisa, IT) Andrea Bracciali (University of Pisa, IT) Nicola Cannata (CO-CHAIR - University di Camerino, IT) Luca Cardelli (Microsoft Research Cambridge, UK) Matteo Cavaliere (Microsoft Research - University of Trento CoSBi, IT) Gabriel Ciobanu (Romanian Academy, RO) Federica Ciocchetta (University of Edinburgh, UK) Flavio Corradini (University di Camerino, IT) Mark Daley (University of Western Ontario, CA) Vincent Danos (CNRS, University Paris Diderot, FR) Pierpaolo Degano (University di Pisa, IT) Mark d'Inverno (Goldsmiths College London, UK) Michael Domaratzki (University of Manitoba, CA) Anthony Finkelstein (University College London, UK) Radu Grosu (Stony Brook University, US) Jane Hillston (University of Edinburgh, UK) Anna Ingolfsdottir (Reykjavik University, IS) Mathias John (University of Rostock, DE) Andrea Maggiolo-Schettini (University of Pisa, IT) Vincenzo Manca (University of Verona, IT) Emanuela Merelli (CO-CHAIR - University di Camerino, IT) Ian McQuillan (University of Saskatchewan, CA) Alberto Policriti (University of Udine, IT) Corrado Priami (Microsoft Research - University of Trento CoSBi, IT) Alessandro Romanel (Microsoft Research - University of Trento CoSBi, IT) Paul Ruet (University of Marseille, FR) Carron Shankland (University of Stirling, UK) Scott Smolka (Stony Brook University, US) Susan Stepney (University of York, UK) Adelinde Uhrmacher (University of Rostock, DE) Irek Ulidowski (CO-CHAIR - University of Leicester, UK) Cristian Versari (University of Bologna, IT) INVITED SPEAKERS: To be announced CONTACT: fbtc2008 AT mcs.le.ac.uk WORKSHOP ORGANISERS: Nicola Cannata and Emanuela Merelli Department of Mathematics and Computer Science University of Camerino Via Madonna delle Carceri 9 I-62032 Camerino (MC) Italy Irek Ulidowski Department of Computer Science University of Leicester University Road Leicester, LE1 7RH United Kingdom From proteininteraction from gmail.com Thu Jan 17 04:36:47 2008 From: proteininteraction from gmail.com (Simon) Date: Thu Jan 17 09:57:05 2008 Subject: [Computational-biology] Call for Chapters for book Biological Data Mining in Protein Interaction Networks Message-ID: Biological Data Mining in Protein Interaction Networks A book edited by X.-L. Li and S.-K. Ng, Institute for Infocomm Research, Singapore Introduction The cellular machinery is a complex system with a multitude of bio- molecular interactions. Most of the cellular processes are mediated by protein-protein interactions (PPIs). Recently, high-throughput methods for detecting PPIs have revealed global pictures of protein interactions on a genomic scale, making it possible to interrogate the interplay of the bio-molecules in carrying out critical life processes at the networked co-operative level. As a result, modern biology's focus has shifted from scrutinizing single molecules to analyzing large complex networks. The Overall Objective of the Book Genome-wide screenings of PPIs can be represented as large protein interaction networks (PINs) in which the nodes represent individual proteins, and the links represent the existence of biological interactions between the corresponding pairs of proteins. In this book, we will present bioinformatics methods that are designed for the computational analyses of the PINs to better understand critical life processes such as the cellular signaling, molecular trafficking, and gene regulatory pathways. Each of the chapters will serve as a tutorial for network-based computational analysis PINs. The objective of this book is to disseminate the research results and best practice from researchers and practitioners working on bioinformatics, data mining, and proteomics. We aim to present the various methodologies in an accessible way to our inter-disciplinary audience, through which we hope to bring better awareness of this interesting and c! hallenging problem to inspire new solutions and applications. The Target Audience The book is aimed at three overlapping audiences: (1) Researchers in the areas of bioinformatics, data mining, machine learning and data structure; (2) Practitioners in the industry in these areas; (3) Instructors and postgraduate students in colleges and universities. This book will be an essential resource for professionals and researchers who wish to learn about the application of advanced data mining techniques in protein interaction networks. In addition, it can be used as a reference for Masters and Ph.D. students studying bioinformatics. Recommended topics include, but are not limited to, the following: Understanding the Properties of a Protein Interaction Network Protein Interactions: Importance and Detection Protein Interactions: In Silico Prediction Interacting Domain Prediction and Usage Interacting Motif: Prediction and Usage Lethal Proteins: Roles and Identification Protein Function: Classification and Annotation Protein Complexes: Construction via Computational Means Functional Module: Detection and Biological Significance Network Motif: Detection and Biological Relevance Network Cleansing: Reliable Interaction Network Conserved Network: Data Mining Across Species PPI and Diseases: Mining Disease Genes from Protein Interaction Networks Computational Analysis for Cell Signaling Computational Analysis for Molecular Trafficking Computational Analysis for Receptor Applications Integrating Protein Interaction Network with Other Biological Resources Submission Procedure Researchers and practitioners are invited to submit on or before March 31, 2008, a 2-5 page manuscript proposal clearly explaining the mission and concerns of the proposed chapter. Authors of accepted proposals will be notified by April 10, 2008 about the status of their proposals and sent chapter organizational guidelines. Full chapters are expected to be submitted by May 31, 2008. All submitted chapters will be reviewed on a double-blind review basis. The book is scheduled to be published by IGI Global, www.igi-global.com, publisher of the IGI Publishing (formerly Idea Group Publishing), Information Science Publishing, IRM Press, CyberTech Publishing, Information Science Reference (formerly Idea Group Reference), and Medical Information Science Reference imprints. Inquiries and submissions can be forwarded electronically (Word document) or by mail to: Dr. Xiao-Li Li Data Mining Department Institute for Infocomm Research 21 Heng Mui Keng Terrace, Singapore 119613 Tel: 65 68748452 * Fax: 65 67768109 E-mail: xlli@i2r.a-star.edu.sg Website: http://www1.i2r.a-star.edu.sg/~xlli/PPI_BOOK.html From jeedward from gmail.com Tue Jan 22 07:01:07 2008 From: jeedward from gmail.com (john) Date: Tue Jan 22 12:23:19 2008 Subject: [Computational-biology] BCBGC-08 Final call for papers Message-ID: BCBGC-08 Final call for papers The 2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) (website: www.PromoteResearch.org ) will be held during July 7-10 2008 in Orlando, FL, USA. We invite draft paper submissions. The conference will be held at the same time and place where several other major events are taking place. The website contains more details. Sincerely John Edward From jeedward from gmail.com Tue Jan 22 07:00:14 2008 From: jeedward from gmail.com (john) Date: Tue Jan 22 12:23:29 2008 Subject: [Computational-biology] MULTICONF-08 Final call for papers Message-ID: <9093838b-1565-4bda-94cf-c8b18e6fdeac@y5g2000hsf.googlegroups.com> MULTICONF-08 Final call for papers The 2008 MULTICONF (website: www.PromoteResearch.org ) will be held during July 7-10 2008 in Orlando, FL, USA. We invite draft paper submissions and the deadline for paper submission is very close. The event consists of the following conferences. * International Conference on Artificial Intelligence and Pattern Recognition (AIPR-08) * International Conference on Automation, Robotics and Control Systems (ARCS-08) * International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) * International Conference on Enterprise Information Systems and Web Technologies (EISWT-08) * International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-08) * International Conference on Software Engineering Theory and Practice (SETP-08) * International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-08) The website contains more details. Sincerely John Edward From thulsen from gmail.com Fri Jan 25 10:02:46 2008 From: thulsen from gmail.com (thulsen@gmail.com) Date: Fri Jan 25 12:22:52 2008 Subject: [Computational-biology] BioVenn - A web application for the comparison and visualization of biological lists using area-proportional Venn diagrams Message-ID: We designed an easy-to-use web application named BioVenn to summarize the overlap between two or three lists of identifiers, using area- proportional Venn diagrams. This very useful tool can be found at http://www.cmbi.ru.nl/biovenn Kind regards, Tim Hulsen. From asidhu from biomap.org Sat Jan 26 04:50:33 2008 From: asidhu from biomap.org (Amandeep Sidhu) Date: Sat Jan 26 13:50:22 2008 Subject: [Computational-biology] 3rd Special Track on Ontologies for Biomedical Systems for 21st CBMS 2008 Message-ID: <2dbc82b00801260150g2ea6aafdi578170c76fe85914@mail.gmail.com> 3rd Special Track on Ontologies for Biomedical Systems for 21st IEEE International Symposium on Computer-Based Medical Systems http://cbms08.biomap.org/ Call for Papers Biomedical Ontologies have developed in an uncoordinated way, often reflecting mere relations of 'association' between what are called 'concepts', and serving primarily the purposes of information extraction from on-line biomedical literature and databases. In recent years, we have learned a great deal about the criteria which must be satisfied if ontology is to allow true information integration and automatic reasoning across data and information derived from different sources. The goal of this track is to survey existing biomedical ontologies and reform them in such a way as to allow true information integration in biomedical domain. Authors are invited to submit original papers exploring the theories, techniques, and applications of biomedical ontologies. Papers are invited (but not limited) to the following themes: * Biomedical Ontologies for Genetics, Proteomics, Diseases, Privacy etc. * Conceptual Models for Biological and Medical Data * Semantics in Biological Data Modeling * Use of semantics to manage Interoperation in Biomedical Databases * Semantic Web technologies and formalisms for Biomedical Data * Ontology representation and exchange languages for bioinformatics * Biomedical Ontologies and OWL * Biological Data Integration and Management using Ontologies * Biomedical Data Engineering using Ontologies * Application of Biomedical Ontologies for Heterogeneous Database Access * Query Optimization Techniques for Biomedical Database using Ontologies * Support of Ontologies for Biological Information Retrieval and Web Services * Change Management in Biomedical Ontologies * Tools for Development and Management of Biomedical Ontologies Important Dates 04 February 2008 Paper Submission Due 28 February 2008 Notification of acceptance 28 March 2008 Final camera-ready paper due 28 March 2008 Pre-registration deadline Paper Submission Procedures Submitted papers have to be original, containing new and original results. Use a maximum of 6 pages IEEE two-column format, including figures and references. All submissions will be done electronically via the CBMS 2008 web submission system (http://www.easychair.org/conferences/?conf=CBMS2008). Submission implies the willingness of at least one of the authors to register and present the paper at the CBMS 2008 Symposium. All papers will be peer reviewed by at least two independent referees. All accepted papers will be included in the conference proceedings. High Quality submissions will be published in a special issue of Biomedical Ontologies Journal by Oxford University Press. Track Organizers Amandeep S. Sidhu Curtin University of Technology, Perth http://www.amandeep.org/ Tharam S. Dillon Curtin University of Technology, Perth Jake Chen Indiana University, USA http://informatics.iupui.edu/people/profile.php?id=74 Elizabeth Chang Curtin University of Technology, Australia http://www.fit.cbs.curtin.edu.au/~chang/docs/index.php Program Committee Alexey Tsymbal (Siemens, Germany) David Hansen (e-Health Research Centre, CSIRO, Australia) David Taniar (Monash University, Australia) Ernesto Damiani (Computer Science Department, Milan University, Italy) Fabio Porto (Database Laboratory, EPFL, Switzerland) Farookh K. Hussain (Curtin University of Technology, Australia) Fedja Hadzic (University of Technology Sydney, Australia) Huiru Zheng (University of Ulster, UK) Jake Chen (Indiana University, USA) James Geller (New Jersey Institute of Technology, USA) Jason Wang (New Jersey Institute of Technology, USA) Li Liao (University of Delaware, USA) Ling Feng (Tsinghua University, China) Maja Hadzic (Curtin University of Technology, Australia) Midori Harris (GO Consortium, European Bioinformatics Institute) Mustafa Jarrar (Vrije Universiteit Brussel, Belgium) Robert Meersman (Vrije Universiteit Brussel, Belgium) Silke Eckstein (Technical University of Braunschweig, Germany) Sourav S Bhowmick (Nanyang Technological University, Singapore) Sun Kim (School of Informatics, Indiana University, USA) Wenny Rahayu (La Trobe University, Australia) Werner Ceusters (New York State Center of Excellence in Bioinformatics & Life Sciences, USA) Yi Pan (Georgia State University, USA) From shandar from nibio.go.jp Sun Jan 27 01:53:25 2008 From: shandar from nibio.go.jp (Shandar Ahmad) Date: Sun Jan 27 13:15:47 2008 Subject: [Computational-biology] PRIB 2008 Message-ID: <1201416805.31793.9.camel@boe> ******* Our apologies if you received multiple copies *********** If you wish not to receive PRIB 2008 related emails, please write to Madhu Chetty and CC to me at shandar@nibio.go.jp ****************************************************************** PRELIMINARY CALL FOR PAPERS AND INVITED SESSIONS ******************************************************************************************** Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008) October 15 ? 17, 2008 Melbourne, Australia http://www.infotech.monash.edu.au/prib08 ******************************************************************************************** PRIB 2008 is aimed at bringing together top researchers, practitioners, and students from around the world to discuss the applications of pattern recognition methods in the field of bioinformatics to solve problems in life sciences. Pattern recognition techniques of interest include: statistical, syntactic, and structural approaches, Bayesian, hidden Markov and graphical models, neural networks, fuzzy and genetic algorithms, data mining, and their hybrids. Papers in areas of (but not limited to) bio-sequence analysis, gene and protein expression analysis, structure prediction, protein folding, docking, metabolic pathway analysis and regulatory networks, system biology, drug design, and bioimaging, are solicited for presentation at the conference. All papers will be peer reviewed and accepted papers will be published in the conference proceedings as an edited volume in Lecture Notes in Bioinformatics by Springer. Submission of papers will be electronic and through the conference website. Proposals for special sessions and tutorials at the conference are also invited in all related areas of research. Authors of selected papers presented at the conference will also be invited for publication in Special Issues of reputed journals. Location: Melbourne is a sophisticated city in the south-east corner of mainland Australia. It is known for its attractive site seeing places, great events, passion for food and wine and fabulous scenery. Boasting as a style-setter, Melbourne is home to continuous program of festivals, art exhibitions and musical extravaganzas. Warning: you might never want to go home. For latest information on PRIB 2008, visit the conference web site: http://www.infotech.monash.edu.au/prib08 or email the secretariat at prib2008.melb@infotech.monash.edu.au Important Deadlines Paper submission: 15 April 2008 Proposals for Special Sessions/Tutorials: 15 March 2008 Author notification: 15 May 2008 Camera-ready papers: 15 June 2008 Organising Committee, PRIB 2008 From tavares from fe.up.pt Sun Jan 27 10:59:27 2008 From: tavares from fe.up.pt (tavares@fe.up.pt) Date: Sun Jan 27 13:22:33 2008 Subject: [Computational-biology] Workshop "Medical Imaging Systems" within EUROMEDIA 2008 - Last Call for Papers Message-ID: ----------------------------------------------------------------------------------------------------------------------------------------- (Apologies for cross-posting) Workshop "Medical Imaging Systems" within EUROSIS EUROMEDIA 2008 April 9-11, 2008, University of Porto, Porto, Portugal http://www.eurosis.org/cms/index.php?q=node/461 We would appreciate if you could distribute this information by your colleagues and co-workers. ----------------------------------------------------------------------------------------------------------------------------------------- Dear Colleague, In recent years, extensive research has been performed to develop more and more efficient and powerful medical imaging systems. Such systems are crucial for medical specialists, allowing a deeper analysis and to understand what is going inside the human body, and therefore they play an essential role for adequate medical diagnosis and treatments. To accomplish efficient and powerful medical imaging systems, many research works have being done in many domains, like the ones related with medical image devices, signal processing, image processing and analysis, biomechanical simulation and data visualization. The main goal of the Workshop "Medical Imaging Systems" is to bring together researchers involved in the related domains, in order to set the major lines of development for the near future. Therefore, the proposed Workshop will consist of researchers representing various fields related to Medical Devices, Signal Processing, Computational Vision, Computer Graphics, Computational Mechanics, Scientific Visualization, Mathematics and Medical Imaging. The Workshop endeavours to contribute to obtain better solutions for more efficient and powerful medical imaging systems, and attempts to establish a bridge between clinicians and researchers from these diverse fields. The proposed Workshop will cover topics related with medical imaging systems, such as: image acquisition, signal processing, image processing and analysis, modelling and simulation, computer aided diagnosis, surgery, therapy, and treatment, computational bioimaging and visualization, software development, virtual reality and telemedicine systems and their applications. Due to your research activities in the field, we would like to invite you to submit a contributed paper. Your contribution is mostly welcomed and we would be honoured if you could participate in EUROMEDIA 2008. DEADLINE FOR PAPERS SUBMISSION: February 5, 2008 SCIENTIFIC COMMITTEE: Alberto De Santis, Universit? degli Studi di Roma "La Sapienza", Italy Ana Mafalda Reis, Instituto de Ci?ncias Biom?dicas Abel Salazar, Portugal Arrate Mu?oz Barrutia, University of Navarra, Spain Behnam Heidari, University College Dublin, Ireland Bernard Gosselin, Faculte Polytechnique de Mons, Belgium Chandrajit Bajaj, University of Texas, USA Christos E. Constantinou, Stanford University School of Medicine, USA Daniela Iacoviello, Universit? degli Studi di Roma "La Sapienza", Italy Dinggang Shen, University of Pennsylvania, USA Djemel Ziou, University of Sherbrooke, Canada Gerald Schaefer, Aston University, UK Jo?o Krug Noronha, Dr. Krug Noronha Clinic, Portugal Jo?o Manuel R. S. Tavares, Faculty of Engineering of University of Porto, Portugal Jo?o Paulo Costeira, Instituto Superior T?cnico, Portugal Jorge M. G. Barbosa, Faculty of Engineering of University of Porto, Portugal Lyuba Alboul, Sheffield Hallam University, UK Manuel Gonz?lez Hidalgo, Balearic Islands University, Spain Maria Elizete Kunkel, Universit?t Ulm, Germany M?rio Forjaz Secca, Universidade Nova de Lisboa, Portugal Miguel Angel L?pez, Faculty University of Ciego de Avila, Cuba Miguel Velhote Correia, Faculty of Engineering of University of Porto, Portugal Patrick Dubois, Institut de Technologie M?dicale, France Reneta Barneva, State University of New York, USA Renato M. Natal Jorge, Faculty of Engineering of University of Porto, Portugal Sabina Tangaro, University of Bari, Italy Valentin Brimkov, State University of New York, USA Yongjie Zhan, Carnegie Mellon University, USA For further details please see the conference website at: http://www.eurosis.org/cms/index.php?q=node/461 We are looking forward to see you in Porto next April. Kind regards, Jo?o Manuel R. S. Tavares University of Porto tavares@fe.up.pt www.fe.up.pt/~tavares From prash from ruc.dk Tue Jan 29 10:17:05 2008 From: prash from ruc.dk (Prash) Date: Tue Jan 29 13:02:42 2008 Subject: [Computational-biology] Positions in Applied Computational Biology and Bioinformatics - University of Manchester Message-ID: <1201619825.479f43717006f@webmail.ruc.dk> There are four positions in computational biology are now available at the Paterson Institute. The Paterson Institute is a leading cancer centre of excellence core-funded by Cancer Research UK and is an Institute of The University of Manchester. We are seeking motivated scientists interested in joining the ACBB group and applying state of the art techniques (see for example, xmap.picr.man.ac.uk) to integrate, analyse and interpret datasets arising from the latest generation of microarrays (including exon, SNP and tiling arrays), quantitative mass-spectrometry and next generation sequencing. The positions available are: * Postdoctoral Scientist - specialist in transcription * Postdoctoral Scientist - pathway specialist * Postdoctoral Scientist - specialist in sequence analysis * Bioinformatics Programmer For further Information see: http://bioinformatics.picr.man.ac.uk Courtesy:_______________________________________________ SocBiN mailing list SocBiN@sbc.su.se https://mail.sbc.su.se/mailman/listinfo/socbin Prashanth Suravajhala PhD Fellow http://ruc.dk/~prash/ ?Difference of opinion shouldnot lead to difference of mind. Half the problems of our life will not arise at all if we remember this? ~~ C B Satpathy From prash from ruc.dk Tue Jan 29 11:06:26 2008 From: prash from ruc.dk (Prash) Date: Tue Jan 29 13:02:53 2008 Subject: [Computational-biology] Resources for the Development of Early-Career Scientists Message-ID: <1201622786.479f4f0240659@webmail.ruc.dk> http://www.hhmi.org/resources/labmanagement/ Courtesy: MentorNet Prashanth Suravajhala PhD Fellow http://ruc.dk/~prash/ ?Difference of opinion shouldnot lead to difference of mind. Half the problems of our life will not arise at all if we remember this? ~~ C B Satpathy From hra from pixel.cviog.uga.edu Thu Jan 31 22:24:59 2008 From: hra from pixel.cviog.uga.edu (Hamid R. Arabnia) Date: Fri Feb 1 15:48:11 2008 Subject: [Computational-biology] Call For Papers: Computer Science & Computer Engineering Conferences - July 2008, USA, WORLDCOMP'08 Message-ID: <20080201033250.0F0968D946E@pixel.cviog.uga.edu> Dear Friends and Colleagues: Please disseminate the following announcement to those who may be interested; I would be most grateful. The deadline for the submission of papers is Feb. 25, 2008. Thank you, Hamid ----- CALL FOR PAPERS WORLDCOMP'08 The 2008 World Congress in Computer Science, Computer Engineering, and Applied Computing July 14-17, 2008, Las Vegas, USA (composed of 25 Joint Conferences) Academic Sponsors: Three technical chapters of IEEE, Research labs at: Harvard University, MIT, UCLA, Georgia Institute of Technology, University of Texas at Austin, University of Iowa, University of Minnesota, University of Illinois at Urbana-Champaign, Emory University, University of North Dakota, PSU/Saudi, Russian Academy of Sciences, and others (see below). Corporate sponsors include Google and NIIT. You are invited to submit a paper for consideration. All accepted papers will be published in the respective conference proceedings. The 2008 World Congress in Computer Science, Computer Engineering, and Applied Computing (WORLDCOMP'08) is composed of the following 25 conferences (all will be held simultaneously, same location and dates: July 14-17, 2008, USA): o BIOCOMP'08: The 2008 International Conference on Bioinformatics and Computational Biology o CDES'08: The 2008 International Conference on Computer Design o CGVR'08: The 2008 International Conference on Computer Graphics and Virtual Reality o CIC'08: The 2008 International Conference on Communications in Computing o CSC'08: The 2008 International Conference on Scientific Computing o DMIN'08: The 2008 International Conference on Data Mining o EEE'08: The 2008 International Conference on e-Learning, e-Business, Enterprise Information Systems, and e-Government o ERSA'08: The 2008 International Conference on Engineering of Reconfigurable Systems and Algorithms o ESA'08: The 2008 International Conference on Embedded Systems and Applications o FCS'08: The 2008 International Conference on Foundations of Computer Science o FECS'08: The 2008 International Conference on Frontiers in Education: Computer Science and Computer Engineering o GCA'08: The 2008 International Conference on Grid Computing and Applications o GEM'08: The 2008 International Conference on Genetic and Evolutionary Methods o ICAI'08: The 2008 International Conference on Artificial Intelligence o ICOMP'08: The 2008 International Conference on Internet Computing o ICWN'08: The 2008 International Conference on Wireless Networks o IKE'08: The 2008 International Conference on Information and Knowledge Engineering o IPCV'08: The 2008 International Conference on Image Processing, Computer Vision, and Pattern Recognition o ITSL'08: The 2008 International Conference on Information Theory and Statistical Learning o MLMTA'08: The 2008 International Conference on Machine Learning; Models, Technologies and Applications o MSV'08: The 2008 International Conference on Modeling, Simulation and Visualization Methods o PDPTA'08: The 2008 International Conference on Parallel and Distributed Processing Techniques and Applications o SAM'08: The 2008 International Conference on Security and Management o SERP'08: The 2008 International Conference on Software Engineering Research and Practice o SWWS'08: The 2008 International Conference on Semantic Web and Web Services (a link to each conference's URL can be found at http://www.world-academy-of-science.org) PURPOSE/HISTORY: This set of joint conferences is the largest annual gathering of researchers in computer science, computer engineering and applied computing. Many of the 25 joint conferences in WORLDCOMP are the premier conferences for presentation of advances in their respective fields. We anticipate to have 2,600 or more attendees from over 80 countries participating in the 2008 joint conferences. The motivation is to assemble a spectrum of affiliated research conferences into a coordinated research meeting held in a common place at a common time. The main goal is to provide a forum for exchange of ideas in a number of research areas that interact. The model used to form these annual conferences facilitates communication among researchers from all over the world in different fields of computer science, computer engineering and applied computing. Both inward research (core areas of computer science and engineering) and outward research (multi-disciplinary, inter-disciplinary, and applications) will be covered during the conferences. WORLCOMP'08 will be composed of research presentations, keynote lectures, invited presentations, tutorials, panel discussions, and poster presentations. In recent past, keynote and/or tutorial speakers included: Prof. Michael J. Flynn (Stanford U.); Prof. John H. Holland (U. of Michigan, Ann Arbor); Prof. H. J. Siegel (Colorado State U.); Prof. Barry Vercoe (MIT); Prof. Ruzena Bajcsy (U. of California, Berkeley); Prof. David Cheriton (Stanford U.), Prof. A. K. Dunker (Indiana U. and Purdue U.); Prof. Jun Liu (Harvard U.); Dr. Jim Gettys (developer of X Window, ...); Dr. Chris Rowen (President and CEO, Tensilica, Inc.); and many other distinguished speakers. FEATURED 2008 KEYNOTE LECTURES: Prof. David A. Patterson University of California at Berkeley, California, USA Member, National Academy of Engineering Member, National Academy of Sciences Fellow of IEEE, ACM, and AAAS Shared (with John Hennessy) the IEEE John von Neumann Medal Prof. Ophir Frieder Georgetown University, Washington, DC, USA The Royden B. Davis, SJ, Chair in Interdisciplinary Studies at Georgetown University, IITRI Chair Professor of Computer Science at Illinois Institute of Technology, Director, Information Retrieval lab (IIT) Fellow of IEEE, ACM, and AAAS (in addition to the above, each of the 25 conferences will have at least one keynote and one invited lecture). FEATURED TUTORIAL: Prof. H. J. Siegel Colorado State University, Fort Collins, Colorado, USA Abell Endowed Chair Distinguished Professor of ECE Professor of Computer Science Director, CSU Information Science and Technology Center (ISTeC) Fellow of IEEE and ACM (in addition to the above, there will also be 11 other tutorials). SUBMISSION OF PAPERS: Prospective authors are invited to submit their draft paper (about 5 to 7 pages - single space, font size of 10 to 12) to H. R. Arabnia by Feb. 25, 2008. email submissions in MS document or PDF formats are preferable (Fax or postal submissions are also fine.) All reasonable typesetting formats are acceptable (later, the authors of accepted papers will be asked to follow a particular typesetting format to prepare their papers for publication.) The length of the Camera-Ready papers (if accepted) will be limited to 7 (IEEE style) pages. Papers must not have been previously published or currently submitted for publication elsewhere. The first page of the draft paper should include: title of the paper, name, affiliation, postal address, email address, and telephone number for each author. The first page should also identify the name of the Contact Author and a maximum of 5 topical keywords that would best represent the content of the paper. Finally, the name of the conference that the paper is being submitted to must be stated on the first page. Papers will be evaluated for originality, significance, clarity, impact, and soundness. Each paper will be refereed by two experts in the field who are independent of the conference program committee. The referees' evaluations will then be reviewed by two members of the program committee who will recommend a decision to the chair of the track that the paper has been submitted to. The chair will make the final decision. Lastly, the Camera-Ready papers will be reviewed by one member of the program committee. IMPORTANT DATES: Feb. 25, 2008: Submission of papers (about 5 to 7 pages) March 25, 2008: Notification of acceptance April 25, 2008: Camera-Ready papers and Registration due July 14-17, 2008: The 2008 World Congress in Computer Science, Computer Engineering, and Applied Computing (WORLDCOMP'08 - 25 joint conferences) GENERAL CO-CHAIR / COORDINATOR: Prof. Hamid R. Arabnia Editor-in-Chief, The Journal of Supercomputing (Springer) Vice President, Int'l Society of Intelligent Biological Medicine The University of Georgia Department of Computer Science 415 Graduate Studies Research Center Athens, Georgia 30602-7404, USA Tel: (706) 542-3480 Fax: (706) 542-2966 E-mail: hra@cs.uga.edu MEMBERS OF PROGRAM AND ORGANIZING COMMITTEES: The Program Committee includes members of chapters of World Academy of Science (chapters: supercomputing; scientific computing; AI; imaging science; databases; simulation; software engineering; embedded systems; internet and web technologies; communications; computer security; and bioinformatics.) The Program Committee for individual conferences is currently being compiled. Those interested in joining the Program Committee should email H. R. Arabnia (hra@cs.uga.edu) the following information: Name, affiliation and position, complete mailing address, email address, a short biography together with research interests and the name of the conference offering to help with. Many who have already joined the committees of individual tracks are renowned leaders, scholars, researchers, scientists and practitioners of the highest ranks; many are directors of research laboratories, fellows of various societies, heads/chairs of departments, deans and provosts. LOCATION OF CONFERENCES: The conferences will be held in the Monte Carlo hotel, Las Vegas, Nevada, USA (with any overflows at other near-by hotels). This is a mega hotel with excellent conference facilities and over 3,000 rooms. It is minutes from the airport with 24-hour shuttle service to and from the airport. This hotel has many recreational attractions, including: spa, pools, sunning decks, Easy River, wave pool, lighted tennis courts, health spa, nightly shows, a number of restaurants, ... The negotiated room rate for conference attendees is very reasonable. The hotel is within walking distance from most other attractions. SPONSORS: (this is a partial list) Academic/Technical Co-Sponsors: (a partial list) --> Computational Biology and Functional Genomics Laboratory, Harvard University, Cambridge, Massachusetts, USA --> International Society of Intelligent Biological Medicine --> Horvath Lab, University of California, Los Angeles (UCLA), USA --> Minnesota Supercomputing Institute, University of Minnesota, USA --> Functional Genomics Laboratory, University of Illinois at Urbana-Champaign, USA --> BioMedical Informatics & Bio-Imaging Laboratory, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA --> Intelligent Data Exploration and Analysis Laboratory, University of Texas at Austin, Austin, Texas, USA --> Biomedical Cybernetics Lab, HST of Harvard University and MIT, USA --> Center for the Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, Georgia, USA --> Harvard Statistical Genomics and Computational Laboratory, Harvard University, Cambridge, Massachusetts, USA --> Hawkeye Radiology Informatics, Department of Radiology, College of Medicine, University of Iowa, Iowa, USA --> Medical Image HPC & Informatics Lab (MiHi Lab), University of Iowa, Iowa, USA --> The University of North Dakota, Grand Forks, North Dakota, USA --> PSU - Prince Sultan University --> Institute for Informatics Problems of the Russian Academy of Sciences, Moscow, Russia. --> Telecommunications Task Force of the Intelligent Systems Applications Technical Committee (ISATC) of IEEE Computational Intelligence Society (CIS) --> IEEE Technical Committee on Scalable Computing (IEEE TCSC) --> IEEE Task force of Ubiquitous Intelligent Computing of IEEE Computational Intelligence Society (CIS) Corporate Co-Sponsors: (a partial list) --> Google, Inc. --> NIIT Technologies Other Co-Sponsors: (a partial list) --> High Performance Computing for Nanotechnology (HPCNano) --> International Technology Institute (ITI) --> GridToday --> HPCwire --> Hodges' Health (H2CM), UK