From ediths at botinst.uzh.ch Tue Dec 1 11:00:47 2009 From: ediths at botinst.uzh.ch (Edith Schlagenhauf) Date: Tue, 1 Dec 2009 17:00:47 +0100 (MET) Subject: [BiO BB] 454/Newbler assembly finishing software? Message-ID: Hi, I've got a bunch of output files from a 454/Newbler de novo assembly for a 8 Mb bacterial genome, ie. various SFF/FASTA/ACE files. What are the most appropriate tools/software for viewing/evaluating the results and for finishing rapidly by automation (there are still several hundreds of gaps...)? There is also a cosmid end library available, and various related genomes. TIA for your input, Edith ****************************************** Dr Edith Schlagenhauf Bioinformatics Institute of Plant Biology University of Zurich SWITZERLAND e-mail: ediths AT botinst DOT uzh DOT ch ****************************************** From dan.bolser at gmail.com Wed Dec 2 12:07:35 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 2 Dec 2009 17:07:35 +0000 Subject: [BiO BB] 454/Newbler assembly finishing software? In-Reply-To: References: Message-ID: <2c8757af0912020907q7277f6d1t8928d776bad05a76@mail.gmail.com> 2009/12/1 Edith Schlagenhauf : > Hi, > > I've got a bunch of output files from a 454/Newbler de novo assembly > for a 8 Mb bacterial genome, ie. various SFF/FASTA/ACE files. > > What are the most appropriate tools/software for viewing/evaluating the > results and for finishing rapidly by automation (there are still several > hundreds of gaps...)? > There is also a cosmid end library available, and various related genomes. For manual contig inspection and editing, the 'classic' choice is still consed. I'm not sure but I think that it's about 130 years old... What you could try is mapping all your 454 reads against the related genomes to get a second set of contigs. You can then combine your de-novo and your 'mapping' contigs with a program like minimus2. The cosmid library can be added by a scaffolder like bambus. If you've got money to spend, you could do some low coverage large insert size Illlumina sequencing and try to 'scaffold' the contigs using that data. Else you could try different assembly packages (i.e. Mira, Velvet, CA-BOG, Phrap, etc.), and again try to combine your contig sets with minimus2. Also... (I've just come back from an assembly workshop ;-) You could try walking in the Newbler parameter space and seeing if you can 'improve' the assembly (depending on how you want to judge that). For assessing quality of the assembly, try viewing in Hawkeye, and also running the AMOS validate pipeline. Unfortunately, I don't know of any 'automatic finishing' software... Consed will design primers for you though. Do you really need to finish? Try annotating what you have. Currently SeqAnswers seems the place to ask NGS related questions. But don't forget to put bbb in your sig ;-) Dan. > TIA for your input, > Edith > > > > ****************************************** > Dr Edith Schlagenhauf > Bioinformatics > Institute of Plant Biology > University of Zurich > SWITZERLAND > > e-mail: ediths AT botinst DOT uzh DOT ch > ****************************************** > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From nikpreb at mail.ntua.gr Thu Dec 3 11:17:14 2009 From: nikpreb at mail.ntua.gr (Nikolaos Preve) Date: Thu, 03 Dec 2009 18:17:14 +0200 Subject: [BiO BB] Extended-CFC- Computational and Data Grids:Principles, Designs, and Applications Message-ID: <4B17E48A.5090002@mail.ntua.gr> --------------------------------------------------------------------------- Please accept our apologies if you receive multiple copies of this Call for Chapters --------------------------------------------------------------------------- CALL FOR CHAPTERS Proposal Submission Deadline: -EXTENDED- December 30, 2009 Computational and Data Grids: Principles, Designs, and Applications A book edited by Nikolaos Preve (PhD) National Technical University of Athens, Greece To be published by IGI Global: http://www.igi-global.com/requests/details.asp?ID=748 Introduction Grid computing is the next generation information technology infrastructure that promises to transform the way organizations and individuals compute, communicate and collaborate. Grid computing is an evolution of distributed computing and it refers to a large-scale high-performance computing which combines distributed heterogeneous computing resources and the result is a unique large virtual supercomputer with a vast amount of shared processing power and data storage. Considering the enormous amount of these underutilized computing resources, the necessity of a grid infrastructure is compulsory. A computational grid provides access to users who want to utilize the shared processing resources in order to efficiently apply high throughput applications on distributed machines. The second most common shared resource used in a grid is data storage and it is known as data grid. This type of grid provides distributed storage capacity such as attached memory to the processor, hard disk drives or other types of permanent storage. Grid computing can assist grid users in order to utilize to the maximum computing resources by applying tasks and solving a scientific or technical problem that requires a great number of computer processing cycles or the need to process large amounts of data. Objective of the Book This book aims to provide relevant theoretical frameworks and will cover the latest empirical research findings in the area of grid computing. The goal of this book is to represent theoretical frameworks, methodologies, implementations, and cutting edge research findings with a critical perspective bridging the gap between academia and the latest achievements of the computer industry. It will be written for professionals, as well as students, who are involved or interested in the study, use, design, and development of grid computing and want to improve and empower their understanding of it. Also, this book aims to help researchers and developers understand the basics of the field, to highlight the various developments over the years in the field by giving an in depth analysis of grid networks. Target Audience The target audience of this book will be composed of professionals, engineers, researchers and students who are interested and working in the field of grid computing. Moreover, the book will provide insights and can serve as both literature at an undergraduate level and as an overview of the area. Recommended topics include, but are not limited to, the following: 1. Theories, definitions, methodologies, models, applications, simulations, and architectures relevant to grid computing 2. Implementations of computational grids, data grids, sensor and mobile grids 3. Grid data storage, grid databases, data management, and data mining 4. Indexing and query optimization over grid databases 5. Grid middleware 6. Web services 7. Security, cryptography, and cryptanalysis 8. Artificial intelligence 9. Algorithms 10. Scheduling, resource management, and optimization 11. Workflow and fault tolerance 12. Programming in grid computing 13. Cloud computing and grids 14. Grid computing in scientific problems (i.e. astrophysics, chemistry, economy and finance, electromagnetics, geophysics, meteorology, numerical analysis, statistics) Submission Procedure Researchers and practitioners are invited to submit on or before December 30, 2009, a 1-2 page chapter clearly explaining the mission and concerns of the proposed chapter. We also highly encourage early full chapter submissions. Please include the title of the book in the subject line of your e-mail. Authors will be notified by January 15, 2010 about the status of their proposals and will be sent chapter guidelines. Full chapters are expected to be submitted by March 31, 2010 or earlier. All submitted chapters must not have been published elsewhere and will undergo a double-blind peer review by at least two referees. Contributors may also be requested to serve as reviewers for this project. Publisher This book is scheduled to be published by IGI Global (formerly Idea Group Inc.), publisher of the ?Information Science Reference? (formerly Idea Group Reference), ?Medical Information Science Reference,? ?Business Science Reference,? and ?Engineering Science Reference? imprints. For additional information regarding the publisher, please visit www.igi-global.com. This publication is anticipated to be released in 2010. Important Dates December 30, 2009: Proposal Submission Deadline January 15, 2010: Notification of Acceptance March 31, 2010: Full Chapter Submission June 15, 2010: Review Results Returned August 15, 2010: Final Chapter Submission September 15, 2010: Final Deadline Inquiries and submissions can be forwarded electronically (Word document) or by mail to: Nikolaos Preve (PhD) School of Electrical and Computer Engineering National Technical University of Athens, 15773 Zographou, Greece Tel.: +30 211 770 8053 ? GSM: +30 697 750 4197 E-mail: nikpreb at mail.ntua.gr with cc to: Editorial Board E-mail: editorialt at gmail.com From mourad12345678 at yahoo.com Sun Dec 6 14:18:58 2009 From: mourad12345678 at yahoo.com (Mourad Elloumi) Date: Sun, 6 Dec 2009 11:18:58 -0800 (PST) Subject: [BiO BB] DEXA'10/BIOKDD'10: Call for Papers Message-ID: <728576.16532.qm@web31501.mail.mud.yahoo.com> CALL FOR PAPERS ??????????????????????????????? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2nd International Workshop on ?? Biological Knowledge Discovery and Data Mining (BIOKDD'10) Held in parallel with 21st International Conference on Database and Expert Systems Applications (DEXA?10) www.dexa.org ? Bilbao , Spain August 30-September 3, 2010 With the development of Molecular Biology during the last decades, we are witnessing an exponential growth of both the volume and the complexity of biological data. For example, the Human Genome Project provided the sequence of the 3 billion DNA bases that constitute the human genome. And, consequently, we are provided too with the sequences of about 100,000 proteins. Therefore, we are entering the post-genomic era: after having focused so many efforts on the accumulation of data, we have now to focus as much effort, and even more, on the analysis of these data. Analyzing this huge volume of data is a challenging task because, not only, of its complexity and its multiple and numerous correlated factors, but also, because of the continuous evolution of our understanding of the biological mechanisms. Classical approaches of biological data analysis are no longer efficient and produce only a very limited amount of information, compared to the numerous and complex biological mechanisms under study. From here comes the necessity to use computer tools and develop new in silico high performance approaches to support us in the analysis of biological data and, hence, to help us in our understanding of the correlations that exist between, on one hand, structures and functional patterns of biological sequences and, on the other hand, genetic and biochemical mechanisms. Knowledge Discovery and Data Mining (KDD) are a response to these new trends. Topics of BIOKDD'10 workshop include, but not limited to: ?? ? Data Preprocessing: Data Storage, Representation and Management, Data Cleaning, Feature Extraction, Feature Selection. ? ?? Data Mining:?Biological Data Clustering/Biclustering, Biological Data Classification, Biological Data Regression, Association Rule Learning from Biological Data, Parallel/Cloud/Grid Computing for Biological Data Mining, Text Mining and Application to Biological Sequences, Web Mining and Application to Biological Data, Analysis of Biological Networks. Data Postprocessing: Knowledge Filtering, Knowledge Representation and Visualization, Knowledge Combination and Integration, Error Rates and Numerical Indicators. ? PAPER SUBMISSION DETAILS: Authors are invited to submit electronically original contributions in English. Submitted papers should not exceed 5 pages in IEEE format . All accepted papers will be published in the proceedings of DEXA?10 Workshops with IEEE CSP. One of the authors of an accepted paper must register to DEXA?10 conference and present the paper at BIOKDD?10 workshop. For paper registration and electronic submission see , starting from January 2010. IMPORTANT DATES:????? Submission of Full Papers: March 30, 2010Notification of Acceptance: April 20, 2010 Camera-ready Copies: May 17, 2010 PROGRAM COMMITTEE: Mourad Elloumi, UTIC, University of Tunis, Tunisia (PC Co-Chair) Jin-Kao Hao, LERIA, University of Angers, France (PC Co-Chair) El Ghazali Talbi, University of Lille, INRIA, CNRS, France Albert Y. Zomaya, The University of Sydney, Australia Nadia Pisanti, University of Pisa, Italy Sandrine Dudoit, University of California, Berkeley, USA Raffaele Giancarlo, Universit? degli Studi di Palermo, Italy Francesc Rossell?, University of the Balearic Islands in Mallorca, Spain Gabriel Valiente, Technical University of Catalonia, Spain Giorgio Valentini, Universit? degli Studi di Milano, Italy Matteo R?, Universit? degli Studi di Milano, Italy Pierre Peterlongo, IRISA-INRIA, Rennes, France Alexandros Stamatakis, Technische Universit?t M?nchen, Germany Mohamed Elati, University of Evry Val-d'Essonne, France Michael Ng, Hong Kong Baptist University , Hong Kong Roderic Guigo, Genome Informatics Research Laboratory, Spain Alfredo Pulvirenti, University of Catania, Italy Jason H. Moore, Dartmouth Medical School , USA Dragan Bosnacki, Eindhoven University of Technology, The Netherlands Carlo Cattani, University of Salerno, Italy Giulio Pavesi, Universit? degli Studi di Milano, Italy Luonan Chen, Osaka Sangyo University, Japan Chiara Epifanio, Universit? degli Studi di Palermo, Italy Graziano Pesole, University of Bari, Italy Elena Marchiori, Radboud Universityn, Nijmegen , The Netherlands Alioune Ngom, University of Windsor , Ontario , Canada Giulia Menconi, Istituto Nazionale di Alta Matematica, Roma, Italy Luca Bortolussi, Universit? di Trieste, Italy Jaume Bacardit, University of Nottingham , UK Rosalba Giugno, University of Catania, Italy Oleg Okun, The National Academy of Sciences of Belarus, Belarus Xiangchao Gan, University of Oxford, UK Florin Leon , Technical University of Ia?i, Romania Mihai Horia Zaharia, Technical University of Ia?i, Romania Xingming Zhao, Shanghai University, China ? From dan.bolser at gmail.com Tue Dec 15 16:40:11 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 15 Dec 2009 21:40:11 +0000 Subject: [BiO BB] Fwd: [Sbforum-general] Bioinformatics post-doc position at Dundee In-Reply-To: <4B27C7F0.50006@compbio.dundee.ac.uk> References: <4B27C7F0.50006@compbio.dundee.ac.uk> Message-ID: <2c8757af0912151340obd34548j72090524995df81e@mail.gmail.com> Hi, Is it allowed to post academic jobs to this mailing list? I see there is a commercial jobs listing at Bioinformatics.Org, but I was wondering about non-commercial (academic) positions? Cheers, Dan. ---------- Forwarded message ---------- From: Geoff Barton Date: 2009/12/15 Subject: [Sbforum-general] Bioinformatics post-doc position at Dundee To: sbforum-general at sbforum.org I have a good opportunity for a computational post-doc who would like to work on Next Gen sequence data and see their analyses tested in the lab. Please see the links to the job advert and further particulars on http://www.compbio.dundee.ac.uk The closing date for applications is 15th Jan 2010. With thanks, Geoff. -- Geoff Barton, Professor of Bioinformatics, ?College of Life Sciences University of Dundee, Scotland, UK. ? ? ? ? ?g.j.barton at dundee.ac.uk Tel:+44 1382 385860/388731 (Fax:385764) ? ? www.compbio.dundee.ac.uk The University of Dundee is registered Scottish charity: No.SC015096 _______________________________________________ Sbforum-general mailing list Sbforum-general at sbforum.org http://sbforum.org/mailman/listinfo/sbforum-general_sbforum.org From jeff at bioinformatics.org Wed Dec 16 18:49:20 2009 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 16 Dec 2009 18:49:20 -0500 Subject: [BiO BB] Fwd: [Sbforum-general] Bioinformatics post-doc position at Dundee In-Reply-To: <2c8757af0912151340obd34548j72090524995df81e@mail.gmail.com> References: <4B27C7F0.50006@compbio.dundee.ac.uk> <2c8757af0912151340obd34548j72090524995df81e@mail.gmail.com> Message-ID: <4B297200.40106@bioinformatics.org> Hi Dan, Unfunded or volunteer positions, such as some internships, could be considered general announcements. Otherwise, we consider them to be "jobs," making them more appropriate for the Career Center (http://www.bioinformatics.org/jobs). And we separate job postings from others mainly because we get so many: 40/month currently and as many as 60/month previously. Cheers, Jeff Dan Bolser wrote: > Hi, > > Is it allowed to post academic jobs to this mailing list? I see there > is a commercial jobs listing at Bioinformatics.Org, but I was > wondering about non-commercial (academic) positions? > > Cheers, > Dan. > > > > ---------- Forwarded message ---------- > From: Geoff Barton > Date: 2009/12/15 > Subject: [Sbforum-general] Bioinformatics post-doc position at Dundee > To: sbforum-general at sbforum.org > > > > I have a good opportunity for a computational post-doc who would like > to work on Next Gen sequence data and see their analyses tested in the > lab. > > Please see the links to the job advert and further particulars on > http://www.compbio.dundee.ac.uk > > The closing date for applications is 15th Jan 2010. > > With thanks, > > Geoff. > > -- > Geoff Barton, Professor of Bioinformatics, College of Life Sciences > University of Dundee, Scotland, UK. g.j.barton at dundee.ac.uk > Tel:+44 1382 385860/388731 (Fax:385764) www.compbio.dundee.ac.uk > > The University of Dundee is registered Scottish charity: No.SC015096 > > > _______________________________________________ > Sbforum-general mailing list > Sbforum-general at sbforum.org > http://sbforum.org/mailman/listinfo/sbforum-general_sbforum.org > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 978 621 8258 -- From golharam at umdnj.edu Thu Dec 17 16:15:21 2009 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 17 Dec 2009 16:15:21 -0500 Subject: [BiO BB] BioRPMs Message-ID: <4B2A9F69.4040309@umdnj.edu> For the last 7 years, the Informatics Institute at UMDNJ has developed and provided a valuable resource in the form of well-curated RPMs to the bioinformatics community, http://informatics.umdnj.edu/BioRPMs Although this repository is not unique, it is actively maintained and used within and outside of the Institute with over 700 registered users worldwide. While we would like to continue maintaining this repository, we are unable to do so in its current state. Instead of letting this repository die or become stale, we would like to open it up to the community in an open-source format, allowing anyone to contribute RPMs. We are looking for a handful of people to help curate and maintain this repository, and find a home to host this repository. If you are interested in helping to curate or can assist in locating a permanent hosting site, please contact me for more information. Ryan Golhar, PhD Informatics Institute of NJ golharam at umdnj.edu