Biobase

Learn how BIOBASE can help with your upstream and downstream data analysis

2007-10-30T17:36:00Z

Use ExPlain to perform upstream and downstream analysis of your high throughput data.

2007-10-30T17:15:00Z

BIOBASE to Coordinate EU-backed Project to Develop Technology for Studying Mechanisms of Disease

2007-10-30T17:13:00Z

BIOBASE, a leading provider of knowledge solutions for the life sciences industry, announced that they have received a European Union research contract to develop innovative technology to analyze complex disease mechanisms. The three-year, 3 million Euro project, called Net2Drug, will be coordinated by BIOBASE and developed as a collaboration with several international participants. The projects goal is to create a sophisticated “toolbox” integrating cutting edge bioinformatics, chemoinformatics, and experimental methods to identify potential therapeutic targets.

“Understanding the mechanism of disease is the key to rationalizing drug development. Net2Drug will provide a knowledge-based approach for identifying critical components in the gene regulatory network that accounts for a specific disease,” explains Prof. Edgar Wingender, President and CSO of BIOBASE, “This approach will enable researchers to confidently select promising drug targets and efficiently identify chemical compounds directed against these targets”.

Dr. Alexander Kel, Senior Vice President Research & Development at BIOBASE and project coordinator adds: “Net2Drug will integrate different ‘omics’ datasets such as proteomics and genomics into cohesive networks to facilitate comprehensive understanding of complex human pathologies. Proof-of-concept will be given by applying our technology on certain tumor types, in particular *** cancer.”

The International Net2Drug Consortium

The Net2Drug consortium includes BIOBASE GmbH (Germany) as coordinator, Progenika Biopharma S.L. (Spain), University of Helsinki (Finland), Fraunhofer Institute für Toxikologie und Experimentelle Medizin (Germany), University of Göttingen/Medical School (Germany), Institute of Systems Biology, Ltd, Novosibirsk (Russia), Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow (Russia) Microbiology and Tumor Biology Center (MTC), Karolinska Institute (Sweden), and the CNR-ITB Institute of Biomedical Technologies (Italy).

The European Union’s Sixth Framework Programme (FP6)

Life Sciences, Genomics and Biotechnology for Health is one of seven top priorities of the European Union’s Sixth Framework Programme (FP6). The FP6 objective is to help Europe take advantage of unprecedented opportunities for generating new knowledge and translating it into applications that enhance human health. To this end, fundamental and applied research is supported, with an emphasis on integrated, multidisciplinary, and coordinated efforts addressing the present fragmentation of European research and increase the competitiveness of the European biotechnology industry.

The indicative budget is EUR 2514 million for the period 2002-2006, including up to EUR 475 million for cancer-related research.

BIOBASE’s ExPlain™ Analysis System and TRANSFAC® Database Achieve GeneChip-compatible™ Status with Affymetrix GeneChip® Microarray Platform

2007-10-30T17:11:00Z

WOLFENBÜTTEL, GERMANY and BEVERLY, MA USA - 05/22/2007: BIOBASE announced today that it has joined the Affymetrix GeneChip-compatible Applications Program, and its ExPlain™ Analysis System and TRANSFAC^® database has achieved GeneChip-compatible™ status with the Affymetrix Inc. (Nasdaq: AFFX) GeneChip^® microarray platform. As a GeneChip-compatible software provider, BIOBASE is committed to seamlessly integrating its applications with the Affymetrix GeneChip platform.

BIOBASE’s award winning ExPlain™ Analysis System provides a novel, fully integrated analysis pipeline for explaining biology on the levels of transcription regulation and pathway analysis. In addition, TRANSFAC^® provides data on transcription factors, their experimentally-proven binding sites, and regulated genes. Both products offer the ability to analyze high throughput experimental data such as Affymetrix microarrays for the identification of future research targets.

According to Holger Karas, Senior Vice President of Business Development, “Combining the vast repository of information available in our products with Affymetrix and the GeneChip-compatible Applications Program offers our customers an unparalleled opportunity to advance their current research and quickly develop experimental direction for future study.”

“Affymetrix is pleased to welcome BIOBASE to the family of GeneChip-compatible software providers,” said Steve Lincoln, vice president of Informatics at Affymetrix. "The coupling of the rich content of TRANSFAC with the analytical methods in ExPlain can result in a greater understanding of disease states and their associated biological processes to users of GeneChip microarrays."

ABOUT THE AFFYMETRIX DEVELOPERS’ NETWORK (ADN)

Through one of the largest third-party software developer communities within the life science industry, Affymetrix works with its software developers to provide a broad spectrum of solutions for leveraging gene expression and genetic variation analysis in both biomedical research and development. Membership in ADN is free of charge for both commercial and academic software developers. For more information please visit www.affymetrix.com/genechip/developer. View the GeneChip-compatible Software Solutions Catalog at www.affymetrix.com/genechip/compatible.

About Affymetrix

Affymetrix GeneChip® microarray technology is the industry-standard tool for analyzing complex genetic information. After inventing microarray technology in the late 1980s, Affymetrix scientists have been dedicated to developing innovative products that provide researchers with a more complete view of the genome. These products continue to accelerate genetic research and enable scientists to develop diagnostics and tailor treatments for individual patients by identifying and measuring the genetic information associated with complex diseases.

Today, Affymetrix technology is used by the world’s top pharmaceutical, diagnostic and biotechnology companies, as well as leading academic, government and not-for-profit research institutes. More than 1,500 systems have been shipped around the world and more than 8,500 peer-reviewed papers have been published using the technology.

Affymetrix is headquartered in Santa Clara, Calif., and has manufacturing facilities in Sacramento, Calif., and Singapore. The company has about 1,100 employees worldwide and maintains sales and distribution operations across Europe and Asia. For more information about Affymetrix, please visit the company’s website at www.affymetrix.com.

BIOBASE and Integrated Genomics Ink Curation Agreement

2007-10-30T17:09:00Z

Chicago, IL, Beverly MA, and Wolfenbüttel Germany. Integrated Genomics Inc. and BIOBASE GmbH announced today that they have signed a collaboration agreement to expand and curate Integrated Genomics’ ERGO™ microbial genomic database. BIOBASE scientists in Bangalore, India will add manually-curated functional gene annotations and pathways to the existing ERGO genomic database. This agreement further expands the custom curation services BIOBASE offers its customers.

Currently ERGO contains more than 3.1 million non-redundant gene sequences in 1,242 genomes in the database. These proteins are linked together into more than 6,300 metabolic and non-metabolic pathways which, together with detailed prokaryotic and eukaryotic functional overviews, provide a biochemical and metabolic reconstruction based on each organism’s genome.

“ERGO contains the largest database of annotated microbial genomes. The expert curation from BIOBASE will add additional high quality annotations and pathways, providing a more complete systems level understanding of organism physiology for our customers,” said Dr. Vinayak Kapatral, IG’s Vice President of Business Development.

Scott MacDonald, Manager of Marketing and Communications at BIOBASE added: “Our expertly curated protein and pathway databases combined with our in-silico customer curation services are a natural compliment that will significantly expand the future content of the ERGO system. In addition, this alliance will provide valuable genomic links to our protein data and expand our presence in microbial sciences.”

About BIOBASE GmbH

BIOBASE is the leading provider of biological databases, knowledge tools, and sophisticated software for the life science industry. BIOBASE products are cutting edge and known for their scientific soundness and high quality They include a comprehensive portfolio of powerful database products, as well as customized databases and analysis of customer data with the help of our proprietary resources. The proprietary content of our databases provides the highest-quality data for the customers' analyses.

BIOBASE is headquartered in Wolfenbüttel, Germany and has offices in Beverly, MA, USA and Bangalore, India.

About Integrated Genomics, Inc.

Integrated Genomics provides a full range of products and services to support research in microbial genomics, biochemistry and gene expression. These products and services are based on ERGO™, the most advanced and comprehensive bioinformatics suite for microbial genomics on the market. ERGO contains the largest available integration of microbial genome data, including genome-derived metabolic reconstructions and representing the chemical reaction networks of metabolic pathways.

Integrated Genomics is headquartered in Chicago, Illinois, USA.

BIOBASE reaches milestone of longevity in “young” industry

2007-10-30T04:33:00Z

BIOBASE announced today that it has reached a milestone few other bioinformatics companies have achieved, it is ten years old. This makes it one of the oldest and most respected providers of biological databases in the world.

Founded in 1997 as a partnership between Dr. Thomas Heinemeyer, Holger Karas, Dr. Edgar Wingender, Dr. Ingmar Reuter, the company’s main goal was to provide researchers a means to take advantage of the vast amount of gene expression data being published in the scientific literature. By creating an easy to use, quality-ensured framework to access this immense volume of data, BIOBASE offers scientists the ability to understand connections and discover biological relationships that are easily overlooked using traditional methods.

Since its inception, BIOBASE has always taken a forward thinking approach to product development. Their flagship databases TRANSFAC® and TRANSPATH® on biological networks have been the industry standard since their release. In 2005 the company expanded into protein databases through the acquisition of the well-respected Proteome™ databases which include YPD™ and HumanPSD™. In 2006, the company released ExPlain™, a gene expression analysis system that draws upon the combined power of all of its database products through a powerful proprietary algorithm. ExPlain can help researchers answer critical questions concerning biological processes both observed in their experiments and predicted by the application itself.

Into the future, BIOBASE will continue to provide customers with products that facilitate systems biology research and accelerate a personalized medicine approach to clinical research. In addition, BIOBASE will continue to expand their customized curation and analysis service for their ever expanding customer base.

“I judge the success of our efforts by the response of our customers”, says Dr. Edgar Wingender, BIOBASE President and CSO. “The most respected pharmaceutical, agricultural, biotech and learning institutions in the world utilize our products everyday for their most critical research projects. To me, that speaks volumes about the quality and utility of the products that we have created.”