Industry Track
posted 04 Jul 2007
Industry Track: 01
Scientific Workflow Driven Solutions for Life Sciences: The Next Frontier
Sunday, July 22
3:00 p.m. – 3:25 p.m.
Room: Hall M
Presented by: Deepak Thakkar, SGI
Abstract:
Industry Track: 02
New insights from expression profiling of P. falciparum genome
Sunday, July 22
3:50 p.m. – 4:15 p.m.
Room: Hall M
Presented by: Ashwin Sivakumar, Ocimum Biosolutions Ltd.
Abstract: The parasite Plasmodium is responsible for hundreds of millions of cases of malaria worldwide. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,400 genes, and is the most (A + T)-rich genome sequenced to date. A large proportion of the genes are devoted to immune evasion and host parasite interactions. Many nuclear encoded proteins are targeted to the apicoplast, an organelle involved in isoprenoid and fatty acid metabolism. Here we report further insights into published P. falciparum microarray data using proprietary. The analysis of data provides not only a deeper insight into the timing of transcription of genes, but also a gateway for identification of new vaccine strategies.
Details of the work:
The work discusses a scientific case study in detail using proprietary tools. It will be of interest to a broad range of audience from the functional genomics space and will be an effort to disseminate knowledge in this sector coming in from Industrial R & D efforts.
http://www.iscb.org/cms_addon/conferences/uploaded/css/20070302040246_ashwin.s.pdf
Industry Track: 03
Fast laptopsequenceanalysisusinghi-performancecomputing
Sunday, July 22
4:20 p.m. – 4:45 p.m.
Room: Hall M
Presented by: Jannick D. Bendtsen, CLC bio A/S
Abstract:
Industry Track: 04
Project Prospect: Life Science Informatics at Royal Society of Chemistry Publishing
Sunday, July 22
4:50p.m. – 5:15 p.m.
Room: Hall M
Presented by: Colin R. Batchelor, Royal Society of Chemistry
Abstract: The Royal Society of Chemistry and its predecessor organizations have been publishing journals since 1841. We present our recent work on semantic enrichment of journal articles in chemistry and molecular biology, and concentrate in particular on life science information. We talk about how life science informatics fits into a journals publishing workflow and what benefits it provides for readers, authors and publishers themselves. We will cover the use of chemical named entity recognition (NER) in publishing, developed in cooperation with academic partners at the University of Cambridge, recognition of Gene Ontology and other OBO terms in chemical text and explain why we have chosen to start with GO terms rather than gene/protein names. We intend to discuss OWL in RDF representations of ontologies and their use in RSS feeds. We will also talk about the possibilities for combining standard chemical information retrieval for chemical structures with biology as expressed through GO terms. We also consider some future extensions in terms of further domains for NER and deeper parsing of text.
http://www.iscb.org/cms_addon/conferences/uploaded/css/batchelorc_20070531021136.pdf
Industry Track: 05
WISDOM: a grid-enabled virtual screening initiative
Sunday, July 22
5:20 p.m. – 5:45 p.m.
Room: Hall M
Presented by: Vincent Breton, CNRS-IN2P3
Abstract: WISDOM is a grid-enabled virtual screening initiative to search for new drugs using grid infrastructures. WISDOM has achieved the deployment of very large scale docking on grid infrastructures. A record screening throughput of 100.000 compounds per hour was reached in the last deployment that took place in the fall 2006 on 5000 computers of EGEE and related e-infrastructures. WISDOM has so far focussed on neglected and emerging diseases. For neglected diseases, grid impact comes from the low cost involved with in silico tests. Two large scale deployments in 2005 and 2006 have allowed to produce lar amount of data on 5 malaria targets proposed by biology laboratories around the world. WISDOM addresses also emerging diseases where the grid added value comes from the capacity to mobilize huge resources to evaluate very quickly the impact of mutations. In 2006, impact of 8 point-like mutations of the neuraminidase N1 was studied. It took 2 months alltogether to select 2250 out of the 300.000 compunds for the equivalent of 1 century of computation. The estimated enrichment factor was 111 and 6% of the compounds tested in vitro are active inhibitors. WISDOM is now evolving toward a service for the academic and private laboratories to allow them to dock their targets on the grid. For biology laboratories and SMEs, it is an opportunity to produce a focussed compound library at a low cost in order to prepare in vitro test. The goal of the talk is to present the work accomplished and its business perspectives.
http://www.iscb.org/cms_addon/conferences/uploaded/css/breton_20070528003258.pdf
Industry Track: 06
A Novel Approach for Rapid Mapping and Analysis of Second Generation Sequence Reads
Monday, July 23
9:30 a.m. – 9:55 a.m.
Room: Hall M
Presented by: Arif Anwar, Synamatix
Abstract: Bioinformatics tools that allow rapid mapping, mining and analyses of reads from second generation sequencers have a big impact on applications such as the development of personalised medicines. Rapid cross referencing of clinical patient sequence data back to the human genome is a critical step in SNP discovery and identifying potential disease states. Performance improvements of between 100 to 10,000 fold for comparative and differential genomics and for mapping based genome assembly from 2nd generation sequencers will be reviewed.
http://www.iscb.org/cms_addon/conferences/uploaded/css/patricia_20070528021156.pdf
Industry Track: 07
An Algorithm for Automatic 2D Depiction of Molecules
Monday, July 23
10:00 a.m. – 10:25 a.m.
Room: Hall M
Presented by: Guido Kirsten, Chemical Computing Group AG
Abstract: A comprehensive algorithm for depiction of 2D coordinates of chemical structures as well as interactions between ligands and proteins is described. The methods used represent a significant improvement to the state of the art with regard to molecular connection graphs which pose particular difficulty to most layout efforts. Resulting coordinates are consistently of publication quality for a large subset of chemistry. The algorithm is discussed and application examples are given for small molecules and protein-ligand interactions.
The presentation is available from the author at: wolfram@chemcomp.com
Industry Track: 08
Heuristic rule based protein function prediction for genome scale data sets
Monday, July 23
2:30 p.m. – 2:55 p.m.
Room: Hall M
Presented by: Dieter Maier, Biomax Informatics AG
Abstract: The number of known protein sequences increases much faster than experimental elucidation of protein function is possible. Even manual curation of functions predicted by bioinformatical methods lags far behind covering less than 10% of known protein sequences. We have developed a heuristic rules based method for automatic function prediction that aims to capture the human decision process during manual annotation. While a number of algorithms for automatic function prediction have been presented in the literature, no common benchmark has so far been used to allow comparison of these methods. Therefore, we have evaluated three automatic methods for protein function prediction using the manually annotated Saccharomyces cerevisiae genome as benchmark. Comparing predictions from decision tree, Bayesian network and heuristic rules we find that the heuristic rules provide the highest precision (86,4%) and recall (74,1%) with the given setup. Machine learning derived rules were validated for use as supplement within the heuristic rule set. The heuristic rule set is robust against differences in sequence origin (e.g. procaryotic vs. eucaryotic) and can easily be extended to integrate new information (e.g. from high-throughput experiments).
http://www.iscb.org/cms_addon/conferences/uploaded/css/dieter.maier_20070530103643.pdf
Industry Track: 09
Accelerating Metagenomics and Next-Generation Genomics using FPGAs
Monday, July 23
3:00 p.m. – 3:25 p.m.
Room: Hall M
Presented by: Darryl A. Leon, Active Motif
Abstract: The growth of publicly available sequence repositories and recent drop in sequencing costs has created an increased need for high-throughput sequence comparison and profile matching tools. Over 100 TimeLogic® biocomputing systems (Active Motif, Inc) have been deployed to leverage this data for expanded annotation studies and drug discovery research. Use of Field Programmable Gated Array (FPGA) technology enables researchers to conduct high-throughput genomic analysis while simplifying computational infrastructure and operational costs.
We will review the scientific research projects at our customer sites such as the Department of Energy’s Joint Genome Institute (JGI), Samuel Roberts Noble Foundation, University of Calgary School of Medicine, and Scripps Institute of Oceanography (SIO-MBRD) and describe how TimeLogic’s acceleration technology and workflow software enhanced the computation needs at each organization. The combination of small-footprint FPGA solutions with cost-effective next-generation sequencing platforms enables a broader range of research labs to undertake large-scale metagenomics projects.
http://www.iscb.org/cms_addon/conferences/uploaded/css/leon_20070531165141.pdf
Industry Track: 10
ARTS – Apple Research & Technology Support
Monday, July 23
3:50 p.m. – 4:15 p.m.
Room: Hall M
Presented by: Victor Jaravine, Apple Europe, Ltd
Abstract: Science research in the 21st Century has two vital components: human talent and the technology needed to realize its potential. Apple’s very recent new initiative, the Apple Research & Technology Support (ARTS) program, brings that talent and technology together. It is designed to help Europe’s young scientists achieve their research goals, by giving them the best tools for the task.
Presented will be a brief overview of the program and a compelling example of this program’s success from the Swedish NMR Center in Gotheborg: a “Hyper-dimensional real-time NMR spectroscopy in structural genomics”. Optimized NMR methodology is developed to dramatically speed-up data acquisition in Structural Genomics. By adapting experiments to each individual molecular system it produces accurate and complete spectroscopic information. Signal accuracy is improved using “matched” optimization. The high-resolution and hyper-dimensional features address spectral overlap and ambiguity problems. The technique is integration of rapid collection and concurrent automatic processing/analysis of multidimensional NMR spectra in real-time. The test results for two proteins show smooth saturation-curves for number of detected and assigned peaks as a function of time. In spite of heavy overlap for cyt complete assignment is obtained in 1/100 of the time of conventional approach. Delivered optimization envisaged to considerably enhance performance of automated procedures in high-throughput applications, as these depend critically on quality and completeness of input data. The approach is implemented on commercial NMR spectrometers.
http://www.iscb.org/cms_addon/conferences/uploaded/css/marino.m_20070610090128.pdf
Industry Track: 11
Improving Scientific Intelligence through Integration
Monday, July 23
4:20 p.m. – 4:45 p.m.
Room: Hall M
Presented by: Darryl Gietzen, Accelrys
Abstract:
