One-Day SIGs (Pre-conference) - Friday, July 15, 2010
One-Day SIG (Pre-conference) - Saturday, July 16, 2011
Two-Day SIG - Friday, July 15 and Saturday, July 16, 2011
3Dsig:Structural Bioinformatics & Computational Biophysics
Date: Friday, July 15 - Saturday, July 16, 2011
Day 1 Start time: 9:00 a.m. End time: 5:30 p.m.
Day 1 Dinner/Keynote*: Start time: 6:30 pm. - 9:00 p.m.
Day 2 Start time: 9:00 a.m. End time: 6:30 p.m.
Location: Austria Center Vienna
Room: Hall E1
*Friday, July 15 - 3Dsig Dinner and Evening Presentation included in 3Dsig Satellite Meeting registration
6:30 p.m. Reception (Cash bar)
7:30 p.m. Dinner
3Dsig, a Satellite Meeting of the ISMB/ECCB conference, focused on structural bioinformatics and computational biophysics and has become the largest meeting in this growing field.
Christine Orengo, University College, London
Relevant topics include:
We look forward to meeting you at 3Dsig
Philip E. Bourne
University of California San Diego
Université de Sherbrooke, Canada
The Weizmann Institute
CAMDA 2011 – Critical Assessment of Massive Data Analysis
Date: Friday, July 15 – Saturday, July 16
Start time: 8:30 a.m. - 6:00 p.m.
Location: Austria Center Vienna
We cordially invite you to attend this year's CAMDA.
CAMDA was founded in 2000 to provide a forum for the critical assessment of different techniques used in large-scale data analysis in the life-sciences, such as for high-dimensional gene expression profiling. It aims to establish the state-of-the-art in analysis methods, as well as identify progress and highlight promising directions for future efforts. To this end, CAMDA adopted the approach of a community-wide contest, with the scientific community analysing the same data sets. Researchers worldwide are invited to take the CAMDA challenge, which has become a prominent fixture (cf. Nature Methods 5, 569). Accepted contributions are presented though talks and posters, and the results and methods of the different analyses are discussed and compared at the conference. Typically, well over 100 scientists join us each year.
As a special opportunity this time, we consider the integrated analysis of a particularly rich structured data set that includes gene and miRNA expression, DNA SNPs, copy number variation, and methylation for about 500 matched samples (see Contest pages).
Keynotes by leading researchers in the field provide further focus points for discussion, with both experimental and theoretical issues covered (recent keynote speakers include Mark Gerstein, Eran Segal, John Quackenbush, and Sandrine Dudoit). This year, we already have confirmed contributions by a number of renowned scientists including Terry Speed.
Included in the CAMDA registration is a trip to a local Heuriger country style restaurant/pub owned by the City of Vienna in the lush vineyards just outside town (Weingut Cobenzl).
CAMDA was founded by Simon Lin and Kimberly Johnson at Duke University (Nature 411, 885. Nature 424, 610). In 2006 CAMDA became a roving conference, with recent venues including Valencia and Chicago. This year, we will host CAMDA in Vienna. For the first time, the conference is run as an official Satellite meeting of ISMB/ECCB.
Jaoquin Dopazo, CIPF, Spain, bioinfo.cipf.es
David Kreil, Boku University, Austria, www.bioinf.boku.ac.at
Simon Lin, Northwestern University, U.S.A., www.feinberg.northwestern.edu
Fifth International Workshop on Machine Learning in Systems Biology (MLSB 2011)
Date: Wednesday, July 20 - Thursday, July 21, 2011
Start time: 9:00 a.m.
End Time Wednesday: 5:30 p.m.
End Time Thursday: 4:30 p.m.
Location: Hilton Vienna - Stadtpark
Room: Klimt Ballroom 1
Hilton Hotels Wien
Am Stadtpark 1
Molecular biology and all the biomedical sciences are undergoing a revolution as a result of improved sensorics. This has resulted in the ability to study biological processes in unprecedented detail, with exploding fields sharing the "-omics" suffix in their name. These include in particular epigenomics, genomics, transcriptomics, proteomics and metabolomics, devoted respectively to the examination of the entire systems of the epigenome, genes, transcripts, proteins and metabolites present in a given cell or tissue type. The availability of these new data sources for biological exploration is changing the way research in quantitative biology proceeds. In terms of sheer numbers we are presented with a large amount of data about the operation of an individual cell (with high throughput sequencing terabytes of information). However, given the complexity of the underlying systems, decoding the interactions between all the components within the biological system is still a massive challenge. Machine learning naturally appears as one of the main drivers of progress in this context, where most of the targets of interest deal with complex structured objects: sequences, 2D and 3D structures or interaction networks. Machine learning also offers the promise of combining disparate data sources to gain a better overall picture of the biological system. The MLSB workshop is focussed on the interface between machine learning and systems biology, topics of interest include learning with structured data, graph inference, semi-supervised learning, system identification, and novel combinations of optimization and learning algorithms.
3rd RECOMB Bioinformatics Education (RECOMB-BE 2011) Conference and Meeting of the “Bioinformatics for Biologists” Alliance
Date: Wednesday, July 20 & Thursday, July 21
Start time: Wednesday, July 20: 8:30 a.m. - End time: 7:00 p.m.
Start time: Thursday, July 21: 8:30 a.m. - End time: 1:00 p.m.
Room Location: Klimt Ballroom 3
Hilton Hotels Wien
Am Stadtpark 1
The Third Annual RECOMB Conference on Bioinformatics Education (RECOMB-BE) will be held in Vienna, Austria, July 20-21, 2011 as an ISMB/ECCB 2011 (http://www.iscb.org/ismbeccb2011) satellite meeting. The conference follows the first two RECOMB-BE meetings: http://casb.ucsd.edu/bioed/ and http://casb.calit2.net/bioed10/ . RECOMB-BE 2011 will consist of invited presentations, oral presentations selected from submitted abstracts and papers, a poster session, and discussion panels, all of which focus on improving bioinformatics education.
Partial List: Laurie Heyer (Davidson College), Larry Hunter (University of Colorado), Fran Lewitter (Whitehead Institute for Biomedical Research), Ran Libeskind-Hadas (Harvey Mudd College), Florian Markovetz (Cambridge Research Institute), Bernard Moret (École Polytechnique Fédérale de Lausanne), Tal Pupko (Tel Aviv University), Pavel Pevzner (University of California at San Diego), Ben Raphael (Brown University), Ron Shamir (Tel Aviv University), Beth Simon (University of California at San Diego), Terry Speed (University of California at Berkeley), and Jens Stoye (University of Bielefeld).
Theme and Scope
The goal of RECOMB-BE is threefold: to showcase best practices of teaching bioinformatics ideas to biology undergraduates, to discuss existing challenges in bioinformatics education (with an emphasis on undergraduate education), and to promote collaboration among educators with the aim to develop a mature bioinformatics curriculum. In keeping with the focus on undergraduates, the conference will also showcase selected bioinformatics research projects conducted by undergraduate students.
While biology has been transformed into a computational science in the last decade, the biological curriculum remains largely unchanged with respect to computational issues. The question: “How should we teach bioinformatics to biology students?” has become of the utmost importance, since many universities have not only founded undergraduate bioinformatics programs but are considering the addition of new computational courses to the standard biology curriculum—a change which would represent a dramatic paradigm shift in biology education. However, as the first two RECOMB-BE meetings demonstrated, there is a great divide in how even the world’s top bioinformaticians thought the subject should be taught, and therefore the above pedagogical question has not been answered satisfactorily to date.
RECOMB-BE therefore aims to demonstrate the intricacy, practicality, and beauty of modern bioinformatics at the undergraduate level, and advance the discussion about its curriculum in the biology classroom. For a summary of RECOMB-BE discussions and the educational challenges that lie ahead for bioinformatics, see Computing has changed biology--biology education must catch up (Science 2009, v.325: 541-542).
RECOMB-BE will have a somewhat unusual format, inspired by the biennial mathematical conference called Gathering for Gardner (G4G) At G4G, leading mathematicians give high-school and undergraduate level lectures; the goal of G4G is therefore to present complex mathematical ideas in a simple form. This objective is one for which the bioinformatics community must also strive in order to establish meaningful future collaborations with biologists and to bridge the cultural gap between computational and experimental scientists.
Unlike previous meetings on bioinformatics education, which have focused on how bioinformatics should be taught, RECOMB-BE showcases how leading bioinformaticians actually teach. Speakers will give short, introductory-level lectures, aimed at undergraduates. These lectures will be complemented by discussion panels focusing on existing challenges in bioinformatics education as well as poster presentations given by undergraduate students on their research projects.
"Bioinformatics for Biologists" Textbook Project
The participants of RECOMB-BE in 2009 and 2010 formed the Bioinformatics Education Alliance, a group of sixteen leading bioinformaticians who have recently collaborated to produce a textbook, called Bioinformatics for Biologists (B4B). The first edition of B4B will be published by Cambridge University Press in the summer of 2011, and test copies will be available at ISMB 2011. Please see the official B4B website for more details: http://cseweb.ucsd.edu/~ppevzner/B4B/
B4B is an open project that will be continuously expanded by new chapters. Therefore, RECOMB-BE invites submissions of proposals for new chapters; accepted chapters will be included in the second edition of B4B which is scheduled for publication in 2012 (see “Important Dates” below).
Call for Participation
We invite submissions in four categories:
Selected papers and abstracts in the first three categories will be invited for either oral or poster presentations. Undergraduate bioinformatics research abstracts will be invited for a poster presentation.
Bioinformatics Education Papers should be submitted via the RECOMB-BE website and must be received by May 5, 2010. Each paper should cover a single biological problem and focus on didactic ways to convey the computational ideas needed to address it. Papers should be self-contained and aimed at advanced undergraduate biology students. Submissions that focus either solely on computational topics or solely on biological topics will not be considered. RECOMB-BE imposes no explicit restrictions on format, length, or notation, as we encourage contributors to choose the style they feel is the most appropriate; however, we anticipate that each contributed paper will be at least 10 pages long.
Authors of selected papers will be invited to submit their paper in the journal PLOS Computational Biology (in the Education Article category) as well as a chapter in the second edition of the Bioinformatics for Biologists textbook, which is described above.
Bioinformatics for Biologists(B4B) Chapter Proposals should be submitted via the RECOMB-BE website and must be received by May 15, 2011. Each submission in this category should constitute a brief description of the proposed chapter. Authors of selected proposals will be invited either for oral or poster presentations at RECOMB-BE 2011. In addition, these authors will be asked to submit a full-length chapter for the second edition of B4B shortly after RECOMB-BE. Proposals should cover a single biological problem and focus on didactic ways to convey the computational ideas needed to address it. Submissions that focus either solely on computational topics or solely on biological topics will not be considered. We anticipate that each chapter proposal will be 1-2 pages long.
Bioinformatics Education Abstracts (submitted by educators) should be submitted via the RECOMB-BE web site and must be received by May 20, 2011. Submissions in this category can discuss practice, challenges, or perspectives in bioinformatics education (e.g., curricula, integration of bioinformatics programs, online courses, etc.) or represent a proposal for a short 20-30 minute introductory lecture aimed at undergraduates. We are specifically looking for lectures that begin with a description of an interesting biological problem, such as "Did we evolve from Neanderthals?" and then show how computational techniques can be used to solve this biological problem. Each abstract should be at most 1 page long.
Undergraduate Bioinformatics Research Abstracts (submitted by undergraduates or first-year graduate students reporting their undergraduate work) should be submitted via the RECOMB-BE website and must be received by May 20, 2011. Each abstract should be at most 1 page long.
RECOMB-BE and the Howard Hughes Medical Institute offer travel support to undergraduate students interested in bioinformatics. All undergraduate students are invited to apply for travel support. RECOMB-BE will have a poster session showcasing undergraduate bioinformatics research, and we encourage undergraduate students interested in participation to submit an undergraduate bioinformatics research abstract. Students who submit abstracts will be given a priority with regards to travel support. First-year graduate students who wish to present their undergraduate work are also welcome to apply for travel support. All applications for travel support should be made via RECOMB-BE website.
In addition to supporting undergraduate students, RECOMB-BE also has limited funds to support authors of accepted RECOMB-BE papers and B4B chapter proposals.
RECOMB-BE was founded by Pavel Pevzner (UCSD) and Ron Shamir (Tel Aviv University) in 2009.
RECOMB-BE 2011 Program Committee: Fran Lewitter (Whitehead Institute for Biomedical Research), Ran Libeskind-Hadas (Harvey Mudd College), Pavel Pevzner, (UCSD) and Ron Shamir (Tel Aviv University).
RECOMB-BE Organizing Committee: Phillip Compeau (Chair), Sangtae Kim, and Son Pham.
RECOMB-BE is supported by the Howard Hughes Medical Institute (HHMI), the International Society for Computational Biology (ISCB), and the California Institute for Telecommunications and Information Technologies (CalIT2).
The RECOMB International Conference on Research in Computational Molecular Biology was founded in 1997 to provide a scientific forum for theoretical advances in computational biology and their applications in molecular biology and medicine. The conference arose from the need to advance research on the mathematical and computational side of molecular biology, and today the conference maintains its focus on state-of-the-art computational advances in this field. The 15th Annual RECOMB conference (RECOMB 2011) will be held March 28-31, 2011 in Vancouver, Canada. The conference website can be found at http://compbio.cs.sfu.ca/recomb2011/.
The RECOMB Satellites Series was founded by Pavel Pevzner in 2001. It contains today nine focused meetings covering various specialized aspects of bioinformatics: RECOMB Comparative Genomics, RECOMB Regulatory Genomics, RECOMB Computational Cancer Biology, RECOMB Computational Proteomics, RECOMB SNPs and Haplotypes RECOMB Systems Biology, RECOMB Massively Parallel Sequencing and of course RECOMB Bioinformatics Education.
The AS-SIG look forward to welcoming attendees to a fun filled evening at the Winery Fuhrgassl-Huber in Neustift on Friday, July 15!
AFP/CAFA: The Automated Function Prediction SIG featuring CAFA: Critical Assessment of Function Annotation
Besides the CAFA challenge, the Automated Function Prediction SIG will also include keynote and contributed talks.
Contributed talks are sought in, but not limited to:
The Bio-Ontologies SIG provides a forum for discussion of the latest and most innovative research in the appplication of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. Bio-Ontologies has existed as a SIG at ISMB for 13 years, making it one of the longest running.
At BioRegSIG-2010, researchers considered the problem of “pattern discovery for prediction/identification of functional elements in sequenced genomes.” BioRegSIG-2011 will be broadened to include other topics that are important in regulatory genomics research. Specifically, we envision sessions and plenary talks that address the following topics:
SIG ORGANIZING COMMITTEE
The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. Many open source bioinformatics packages are widely used by the research community across a wide range of application areas. They form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation, dissemination, and wide adoption of new computational methods, reusable software components, and standards. The sessions planned for BOSC 2011 include:
Keynote speakers (as of March 7, 2011):
Lawrence Hunter is Professor of Pharmacology and Computer Science at the University of Colorado and director of the Computational Bioscience Program at the School of Medicine. He is one of the founders of ISMB, a fellow of the ISCB, and well known for contributions in a broad range of problems in computational biology. Dr. Hunter will be giving a talk entitled The role of openness in knowledge-based systems for biomedicine.
As the Technology Evangelist for Amazon Web Services, Matt discusses the technical and organisational aspects of cloud computing across the world. With a background in the life sciences, Matt is interested in helping teams of all sizes bring their ideas to life through technology. Before joining Amazon he built web-scale search engines at Cornell University, sequenced DNA in Hinxton and developed scientific software in Cambridge. He is a frequent speaker at international conferences, a blogger, published author and an advocate of research productivity. Matt's talk, entitled Into the Wonderful, will feature a discussion of the constraints of working with the size, scope and complexity of modern research data, and how cloud computing can help accelerate academic research. We'll take a look at the current state of the art, the role cloud computing plays in increasing the impact of open source tools, the use of public hosted data in the cloud and how academic cloud platforms can help promote collaboration, reproducibility and reuse across disciplines.
Please visit our web site at http://www.open-bio.org/wiki/BOSC_2011 for more details about BOSC 2011.
Start time: 8:30 a.m. - End time: 6:00 p.m.
Room Location: Hall F1 (Austria Center Vienna)
High Throughput Sequencing is revolutionizing the way biologists generate and analyze biological data. While in the past sequencing was used mainly to characterize individual genomes or transcripts, low-cost high-throughput sequencing can now address a broad range of genetic analysis applications including: comparative genomics, high-throughput polymorphism detection, analysis of coding and non-coding RNAs, identifying mutant genes in disease pathways, and profiling metagenomes. Some of the earlier “high-throughput” technologies, such as Illumina, and ABI SOLiD have compromised read length to increase throughput. Forthcoming, 3rd Generation sequencing technologies are expected to have significantly longer reads, albeit at the cost of high error rates, while maintaining, or increasing the overall throughput.
I. Detecting Genome variation
While the problem of mapping reads to a pre-existing “reference” genome is becoming better understood, better algorithms for discovery of important variants from the mapped reads are still necessary. This session will explore methodology to infer various polymorphisms (SNVs, large insertions/deletions, copy number variations) with HTS data. As the HapMap and now the 1000 Genomes projects have increased our understanding of SNPs, structural variation (including insertions, deletions, translocation, inversions, and CNVs) have come to the forefront as one of the main sources of variation within a species. HTS technologies offer the potential of high resolution detection of structural variants, in particular in cancer genomes, but they will also create a deluge of data, requiring the use of more powerful algorithms. The methods for detecting structural variants using HTS data are a promising research area for the genome analysis community.
II. Transcriptome Analysis
Another exciting application of HTS technologies is RNA sequencing. Here the target sequence is not the genome, but the set of RNA molecules transcribed from the genome. RNA sequencing is currently used for several applications, including RNA expression, de-novo transcriptome sequencing for non-model organisms, and novel (coding and non-coding) transcript discovery, among others. For RNA and micro-RNA expression profiling, HTS has significant advantages compared to microarray methods in that it is better able to identify quantities of very common and very rare transcripts. RNA sequencing also makes possible the discovery of novel transcripts, which do not match any probe on a microarray – an important feature for discovery of novel transcripts, and identification of alternative splicing. Transcriptome profiling is also increasingly used for sequencing the RNA of non-model organisms for phylogenetic and population studies, and methods for transcriptome assembly and co-assembly need to be improved. With sequencing, detection of expressed SNVs and their use to detected allele-specific expression and cis-regulatory elements is also feasible. This, again, is a novel area of algorithmic exploration.
III. Epigenomics and chromatin regulation
HTS Sequencing is also commonly used for discovery of transcription factor binding sites (and nucleosome positioning) using CHiP-seq. In addition, many techniques are appearing to explore the epigenome, including methylation sensitive restriction enzymes, MeD-IP, and bisulfate resequencing. The latter makes the problem of aligning reads much more complex. Thus, novel algorithms will be required to handle these experiments.
Another common application of HTS is metagenomics. This ranges from sequencing of environmental samples, to census of microbial flora in disease affected individuals vs. control. We welcome presentations on these topics, as well as any other important methods related to HTS technologies.
V. 3rd Generation Sequencing Technologies
One of the key developments in the HTS field is the emergence of 3rd generation, single molecule sequencing technologies. These promise to enhance the utility of whole genome DNA sequencing and the associated genetic analysis applications by providing longer reads, quicker turnaround times, and valuable kinetic information that enables direct detection of base modifications as part of a sequencing run. The diversity of applications and flexibility of single molecule sequencing technologies will demand novel approaches to modeling sequencing data in order to fully leverage the information (e.g., kinetic information associated with each read) obtained from such platforms. As was the case with other HTS platforms, programs and algorithms developed for Sanger and NGS data will need to be modified or reinvented to match the characteristics of single molecule sequencing data. Managing and organizing the data in ways that facilitate interpretation and data mining applications will also be a challenge.
3. Draft Schedule
9 am – 12 pm Session I, Variation Discovery: Keynote address 1, 7-8 talks
1:30pm - 6 pm Session II, Transcriptomics: ~10 talks
9 am – 12 pm Session III, Epigenetics & Metagenomics: ~10 talks
1:30pm - 4:30 pm Poster Session
5pm – 6pm Keynote address 2
Francisco M. De La Vega
For interactions amongst thousands of genes, proteins, and metabolites, these networks can be quite large and complex. Network analysis tools can manage this complexity, for example by identifying clusters of activity – regions of high interconnectivity that are also characterized by high gene expression levels. The most highly connected molecules or hubs of such regions may be control points for the network; modulating their activity may influence the activity of many other molecules. With knowledge of the structure and behavior of biological networks, biologists can identify intervention points for drugs and therapeutics, limit adverse side-effects of treatments, and infer predisposition to disease.
We are soliciting abstracts that cover new developments in network biology. The SIG will focus on two major areas: (1) the development of network-related tools and resources, and (2) the application of network analysis and visualization in the study of biology, synthetic biology and medicine. The SIG will provide a unique interface between tool developers and users in the field of network biology. Through these complementary lenses, the SIG will bring into focus the current state of the field, its future promise and how to get there.
Diego di Bernardo
SNP-SIG: Identification and annotation of SNPs in the context of structure, function, and disease
The primary goal of the SNP-SIG is to outline and discuss the recent advances in the methodology for the annotation and analysis of genomic variation data.
SNPs are generally very interesting in the context of their phenotypic manifestations. The discrepancy between the significant availability of SNP data and the current lack of its interpretation requires the development of methods for the annotation/prediction of the SNP impact. Direct-to-consumer (DTC) companies, such as 23andMe and Navigenics, offer DNA tests to provide insight on the genetic traits. In the near future the analysis of genetic variation will be a key factor for the understanding of the information encoded in the genome
The SNP-SIG provides a forum necessary for the organization of a research network facilitating the exchange of ideas and the establishment of new collaborations bringing together varying expertise. It will thus support the unprecedented collaborative effort to manage the complexity of the analysis and evaluation of genetic variation.
We are interested in attracting submissions describing original work in all the fields of genomic variation research including, but not limited to: