Abstracts of presentations during the User Group Meeting:
Bayer HealthCare AG
"Integrated Pharma Research IT Platform at Bayer HealthCare AG"
Dr. Michael Härter, Pharma Research, Bayer HealthCare AG, Wuppertal, Germany
As part of an ongoing project in the area of corporate database consolidation and data analysis LION bioscience develops a software for data visualization, data analysis and project tracking that is used within the Pharma Research division of Bayer HealthCare AG. The customer-tailored application is based on the LION Discovery Center (LDC). It combines a true chemistry spreadsheet as the core of the application with various tools and charts for data analysis and visualization as well as tools for drill-down within a hierarchy of data. The application is able to retrieve information from the corporate data warehouse through a proprietary corporate query builder. In addition to other functionality, the software provides access to 3rd party and corporate compute services and stand-alone databases. These computations (or database searches) are triggered from the LDC spreadsheet and the results are fed back to allow for further correlation and interpretation of data. Examples of such external compute services are clustering of chemical structures or calculations of ADME-relevant parameters. In the area of project tracking the application provides a virtual workspace for research projects to be managed and documented – a so-called project teamspace. It allows for intelligent document handling and project organization. An update of the application with extended functionality is currently being deployed to all pharma research scientists at Bayer HealthCare. The presentation will cover some of the functionality of the software and of how it is used within the organization.
"Analysis and annotation of plant sequences"
Christophe Ketterlé, Biogemma
Biogemma is a cropscience research company, working for the improvement of the vegetal species and the protection of the environment. Main studies, that concern gene discovery, are made on maize, wheat, rapeseed, and other large crops. For that purpose bioinformatics have to handle a huge amount of heterogeneous data. We have an integrative platform that offers numerous databases and bioinformatic tools to our biologists. Biologists can easily navigate through ESTs annotation, mapping data, SNPs, genomic data and transcriptome data.
Important part of this environment is SRS which is used to handle our sequences annotation information that is obtained by our own pipelines and also by bioSCOUT.
Note that the switch from bioSCOUT to LION Target Engine has occurred recently in our company.
Biovitrum AB, Sweden
"Running SRS 7 and Prisma on Linux RedHat 8: Biovitrum's Cluster Challenges".
Sarah Hunter, Biovitrum AB, Sweden
With more and more bioinformatics programs only being made available for the Linux platform and a marked shift by hardware vendors towards Linux in general, the purchase of new server technology was deemed necessary at Biovitrum. To simplify server administration and keep the cost of the investment at a minimum, it was decided that SRS/Prisma should run alongside our other in-house bioinformatics software on a single machine. This presentation outlines the installation of SRS on a Linux8 cluster running Platform's LSF. It also covers some of the ideas and suggestions from expert and casual users on how SRS can be improved in the future.
Celera Genomics Inc., USA
"Celera's Customization of SRS and the API"
John P. Carnes-Stines, Celera Genomics Inc., USA
Celera started using SRS with version 6. We've spent a large amount of money and time customizing SRS and the APIs to host our own data as well as to present public datasets in different ways. Through that process, we've learned much about customizing SRS. This presentation will briefly re-introduce our architecture for the portal, describe how we customized it and how we should have customized it. I'll also touch on our experience with SRS running on AIX, and talk a bit about how we're using the SRS APIs to support several services.
ChemNavigator Inc., USA
"Using 3-DPL for Finding Ligand-Target Relationships"
Dr. Tad Hurst, Vice President and CTO, ChemNavigator, Inc., USA
The virtual screening of a large collection of compound candidates against a group of protein targets can be a difficult task for any organization. To address this challenge ChemNavigator has developed an ultra-fast in silico protein-ligand docking system called 3-DPL Map™. The technology is designed to search databases with millions of compounds and to find those compounds most likely bind to a protein and show activity in a biological screen. Using LION’s SRS linking technology in conjunction with manual curation, protein structures can be classified and associated with selected therapeutic areas (e.g., inflammation and immunosuppression). For the initial work, 3-DPL was used to search compounds that dock to the Map Kinase P38 and FKBP12 protein. FKBP12 is part of the Calcineurin/FKBP12 complex, and is reported to be associated with immunosuppression. The 3-DPL search ran for several days using 3.4 million unique drug-like compound structures.
The top compound hits were tested in an independent laboratory, and three of them displayed activities near the 1 mM range. These three compounds were selected as good candidates for further lead optimization and testing. In summary, this approach accelerates the identification of compounds that bind selectively to specific protein targets associated with a particular therapeutic area.
Daylight Chemical Information Systems, Inc., USA
"Retrieving Chemical Data from SRS"
Daylight Chemical Information Systems, Inc., USA
DeltaSoft Inc., USA
"Cheminformatics Software Supporting the Drug Discovery Process"
Dr. Yvonne Shimshock, Manager Business Development, DeltaSoft Inc., USA
European Bioinformatics Institute (EBI), UK
"The EBI's external Services SRS Server"
Rodrigo Lopez, EBI, UK
The most important mission of the EBI is to provide free access to it's growing body of biomolecular databases to all facets of the scientific community in ways that promote scientific progress. The EBI's SRS servers act as central information hubs for internal as well as external users. This presentation will cover new developments and improvements and shed some light into the future of SRS at the EBI.
GPC Biotech AG, Germany
"Using SRS to Build a Comprehensive Sequence Annotation Pipeline"
Dr. Joachim Vogt, Scientist, GPC Biotech AG, Germany
GPC Biotech AG (Martinsried, Waltham, Princeton) has developed a tool called the AnalysisPipeline to automate the characterization of sequence data. Combining this tool with the power of a Linux cluster enables the analysis of large numbers of sequences in a short time frame. In addition the integration of this tool into the SRS interface makes using it as simple as running a blast search. The AnalysisPipeline extracts sequence annotation from SRS using the SRS Objects API which provides access to all the information stored in the SRS system from a programming language like PERL or JAVA. The AnalysisPipeline can be used as a standalone tool, but the integration into a framework of other in-house tools and databases like a LIMS system or a database of experimental information turns it into a annotation service that can be called from multiple applications. Technical aspects of AnalysisPipeline setup as well as some typical application scenarios will be presented.
IFOM - FIRC Institut of Molecular Oncology, Italy
"Bioinformatics Development and SRS: Applications to Microarray Data Annotation and Disease Gene Discovery"
Alessandro Guffanti, MSc, Head of Bioinformatics Services, IFOM - The FIRC Institute of Molecular Oncology, Milano, Italy
The availability of an academic version of the Sequence Retrieval System software has always been a great bonus not only for the average researcher interested in web-based sequence retrieval and analysis, but also for the bioinformatics developer interested in developing new and innovative tools for helping the biological discovery process. Web-based tools implementing the integration of the command-line version of SRS and the PERL scripting language have been developed at IFOM in the recent years and are now freely available from https://bio.ifom-firc.it. The applications using more heavily the integration between SRS, local biological databases and web-based interfaces are:
1) large-scale EST annotation with user-defined fields (The EST Annotation Machine);
2) creation of updated gene annotation tables for a range of popular DNA chips (Automated DNA Chip Annotation Tables);
3) large-scale conversion of generic to universal gene identifiers for Unigene colony picking (The UniGene Machine);
4) automated annotation of potential EST antisense transcripts within a given genomic region (AntiHunter).
The general philosophy and technical details underlying the development, production and maintenance steps of these web-based tools will be illustrated. In addition, the contribution of a series of scripts incorporating large-scale SRS queries to a bioinformatic project for large-scale identification and annotation of chromosomal aberrations in tumors will be described.
LION bioscience Inc., USA
"An In Silico Study of breast cancer associated gene 3 Using LION Target Engine and Other Tools"
Dr. Darryl León, LION bioscience Inc., USA
Sequence analysis of individual drug targets is an important step in annotation and validation. As a test case, we investigated human BCA3 (breast cancer associated gene 3) with the new LION Target Engine™ and with other bioinformatics tools. The LION Target Engine™ confirmed that the BCA3 gene location, and the two most likely splice variants (lacking exon 3, and exons 3 and 5, respectively) exist. It is proposed that an additional variant (missing only exon 5) published in a public sequence repository, is a prediction artifact. A significant number of new orthologs were also identified, and these were the basis for a high quality protein secondary structure prediction. Moreover, our research confirmed several distinct functional domains as described previously in earlier reports. Sequence conservation from multiple sequence alignments, splice variant identification, secondary structure predictions, and predicted phosphorylation sites, suggest that the removal of interaction sites through alternative splicing might play a modulatory role in BCA3. This in silico approach shows the depth and relevance of an analysis that can be accomplished by including a variety of publicly available tools with an integrated and customizable life science informatics platform.
"LION Target Engine™: Highlights and Roadmap"
Dr. Clemens Suter-Crazzolara, Director Product Marketing, LION bioscience AG, Germany
LION Target Engine™ extends the integrative and query capabilities of SRS, so that questions specific in the target identification and validation process can be addressed. LION Target Engine™ is a suite of applications, each of which can be delivered as stand alone. Combined, they optimally help the bench scientists and bioinformaticians to accelerate the pace of their research. For reporting bioinformatics data, each application employs the Summary Sheet, a comprehensive, sharable and easy-to-understand visualization tool.
Currently, about 10 applications are delivered, of which the central data-unifying Gene Hub, the Annotation Component and the Pathway and Protein Interaction Component are the most prominent. Rich APIs ensure optimal connections to legacy tools and databases. In this presentation, LION Target Engine™ will be introduced and future plans will be discussed.
"SRS 8.0 - Making life easier"
LION bioscience Ltd. UK
SRS 8.0 will represent a step change in the technology – moving to standard technology and enabling a greater level of integration with other applications than previously achievable. This Pre-view will discuss the reasons for the change, present the new end-user functionality and address the upgrade from previous versions of the product to the new platform.
"SRS Moving forward"
Nick Murrall, LION bioscience Ltd., UK
The new technology gives LION the platform to move SRS forward in order to address, even more, the needs of the end-user community. The current ideas will be presented in order to gain your feedback and ensure SRS remains a key research tool in your portfolio.
"SRS Gateway for Oracle as an SQL Interface to Flat File Data"
Ken Griffith, LION bioscience Inc., USA
LION and Oracle have jointly developed the ‘SRS Gateway for Oracle’ enabling users to take advantage of the data integration capabilities of the SRS platform from the Oracle SQL environment. Using this new product it is possible to write a SQL query that accesses all of the flat file databanks in an SRS installation along with native Oracle relational tables. The SRS Gateway for Oracle defines a set of tables and columns that can be queried in SRS. These are then mapped to Oracle data types through the Oracle Transparent Gateway technology enabling SQL queries to be translated into SRS queries. This gives Oracle users access to more than 950 public databanks in SRS and other internal data that have been integrated into SRS.
Microsoft Deutschland GmbH, Germany
"Microsoft .Net - The Information Worker in the Pharmaceutical Industry"
Andreas Schulz, Microsoft Deutschland GmbH, Germany
National Taiwan Univesity Hospital
"Applications of Bio-Clinical Informatics – SRS in a medical knowledge management system"
Chee Jen Chang, MS, Ph.D. Associate Director, Clinical Trial Center, National University Hospital
Professor, Graduate Institute of Clinical Medicine / Clinical Pharmacy, National Taiwan University School of Medicine
More and more medical researchers are interested in how to best leverage genomic information in clinical research for the purpose of efficiently conducting clinical trials and to reduce the adverse effects of drugs. Last year’s issuance of guidance by the FDA on the submission of pharmacogenomics data is a milestone towards the trend. This presentation will introduce to the audience concepts for incorporating LION SRS into bio-clinical knowledge management systems, and share our experiences.
Oracle Corporation, USA
"The Oracle Technology Behind the SRS Gateway for Oracle"
Dr. Susie Stephens, Life Sciences Product Manager, Oracle Corporation, USA
The Oracle Transparent Gateway technology is an established feature of the Oracle database that provides the ability to transparently access data in non-Oracle systems from an Oracle environment. This transparency removes the need for application developers to customise their applications to access data from different non-Oracle systems, thus minimising development efforts and maximising the mobility of applications. In addition, this technology takes advantage of the distributed SQL optimisation capabilities of the database, which results in highly performant multi-site queries. This presentation will give an overview of the Oracle Transparent Gateway technology, and describe how LION has taken advantage of this functionality to develop the SRS Gateway for Oracle.
Akzo Nobel N.V. Organon, Netherlands
"SRS customizations at Organon, the versatile character of SRS"
Rene van Schaik, Head of Bioinformatics, Organon, Netherlands
Siena Biotech S.p.A., Siena, Italy
"Make Drug Discovery More Efficient"
Dr. Andreas Kremer, Senior Scientist Bioinformatics, Siena Biotech S.p.A., Siena, Italy
The amount of data and the number of databases used in the biomedical research is constantly growing. Naturally this raises questions regarding the use of this vast amount of information and the quality of the data within the drug discovery process.
At Sienabiotech, we chose LION Target Engine™ and LION DiscoveryCenter™ to integrate all applications and data we use as part of our research activities.
The effective integration of public and proprietary data as well as automatically generated and manually-curated annotations is crucial for us. The "Knowledge Driven" discovery process involves establishing a reasonable disease hypothesis (e.g. pathopathway analysis), determining expression patterns, developing an assay system for screening and importantly establishing whether the target is indeed ‘druggable’ i. e. can be modulated by small molecules.
"Pathway & Interaction Networks in LION Target Engine™"
Dr. Andreas Kremer, Senior Scientist Bioinformatics, Siena Biotech S.p.A., Siena, Italy
Pathway models or protein-interaction networks are excellent tools in the drug discovery process. They can be used to identify and select highly reliable targets for a given disease hypothesis. Combining information from diverse sources (in house experiments as well as literature) potentially transforms protein-interaction networks into detailed descriptions of cellular pathways. Interactive diagrams allow the linking of data directly onto the pathway and in this way can be used to integrate all relevant data regarding a project into one framework.
At Sienabiotech, we started to use the LION Target Engine Pathway Component to support our target identification and validation activities. The pathway diagrams are also used as communication tools, particularly for our interdisciplinary project teams. The diagrams ensure a common understanding and facilitate critical interrogations of disease hypotheses or mode of actions.
Silicon Genetics, UK
"The GeneSpring / SRS Integration"
Neil Ward, Silicon Genetics
Silicon Genetics is the leading provider of software for the analysis of microarray data. Learn how it is possible, via the SRS connector, to integrate the market leading GeneSpring package with the advanced search functionality of SRS. The combination of these sophisticated tools gives unrivalled ability to extract biologically relevant information from all types of laboratory data thereby improving and accelerating your research.
"Successfully deploying Text Mining in the Life Sciences: TEMIS Text Mining Solutions at IPSEN Pharma"
Dr. Charles Huot, CEO, TEMIS Group, France
We describe a case study of a large information management project that TEMIS carried out at the Pharma Research Center Henri Beaufour of IPSEN in Les Ulis near Paris. The modular architecture of the TEMIS software as well as the flexibility to tailor it to specific requirements of the users proved to be essential for the design and implementation of a large-scale indexation and classification system that gives IPSEN's experts access to an immense body of textual information.