Bio Saga Headlines

Bio Saga

Tuesday, August 25, 2009

Researcher at Molecular Connections develop a Alzheimer disease Pathways Compendium for inclusion at the Alzforum

This Pathways Compendium provides an index of Alzheimer disease pathway models contributed by researchers and companies.

Probable Interaction Networks Involved in Pathology of Alzheimer Disease: Predicting Targets and Therapeutic Agents - NetPro™ based Study. Developed by researchers at Molecular Connections Private Limited, an in silico discovery services company. Users can click on a specific node (molecule) to get information on all interactions of the molecule in the given network. Click on the interaction arrows for information on the specific interaction.

The Alzheimer Research Forum is a Pioneering Biomedical Web Community. Founded 13 years ago when the Web was still in its infancy, the "Alzforum" has more than 5,000 registered members and is familiar to most Alzheimer scientists in the world.

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.

Wednesday, August 19, 2009

NIH Program Targets Bioinformatics, Computational Biology Projects

More good news for Bio, more so for Bioinfo & CompBio while the end of Jyly say House Passes Proposed 3 Percent NIH Funding Increase now NIH is really promoting Bio Science research to bring in a economic turn. The best of times is now!

A National Institutes of Health funding program will support exploratory research and development projects in informatics and computational biology that explore a range of areas, including genomics, medical genetics, proteomics, biomedical imaging, and a wide variety of other approaches.

Funded through the National Cancer Institute, the National Human Genome Research Institute, the other centers across NIH, the "Exploratory Innovations in Biomedical Computational Science and Technology" program will be coordinated by the NIH Biomedical Information Science and Technology Initiative committee.

Under the program, NIH will grant up to $275,000 over two years to academic institutes, small businesses, non-profits, state governments, and other groups who will conduct research aimed at rapidly advancing informatics and computational biology goals in database design, querying approaches, data retrieval, visualization, and integration.

Areas of interest include approaches for handling data from genomic sequencing studies, gene expression, proteomics, pathway data, biomedical imaging, and other areas.

NIH said that the program is seeking to fund the development of

  • Tools for data acquisition, archiving, querying, retrieval, visualization, integration and management;
  • Platform-independent translational tools for data exchange and for promoting interoperability;
  • Analytical and statistical tools for interpretation of large data sets;
  • New models or simulations of complex biological processes at single and multiple levels or across multiple scales.

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.

Tuesday, August 11, 2009

Curated databases and data curation

"There does appear to be a distinction between the way curation is used in the bio-sciences, and elsewhere. In particular, the term "curated database" tends to mean a manually constructed database that links literature to data, curated by experts who provide authority (eg see the Wikipedia definition of Biocurator). The earliest mention of the term "curated database" I can find is in the abstract (and only in the abstract) of Larsen et al (1993)." Chris Rusbridge Digital Curation Blog
Since these database are hand curated by experts (manually curated), they always promise a accuracy & quality better than uncurated or NLP based databases. While NLP based databases follow a automated curation provide quick updates and tend to be large in terms of the quantum of data. While they may trade off in accuracy due to their automated curation process.

While platforms like XTractor Premium follow a unique approach by trying to adopt the best of both worlds. A hybrid approach of a first level of NLP which promises a quick turnaround and large quantum of data followed by expert curation to preserve and maintain the high quality promised by expert curated database. XTractor Premium is a specialized biomedical text mining platform with semantically enriched search (Semantic search) and analytics to that enable discovery, knowledge sharing, analysis and modelling of published biomedical facts.

Sunday, August 9, 2009

Search Wars Episode II. Yebol a new search!

One of my recent post discussed the dawn of the new era and new breed of search engines Search Wars.

a youngling from the the Stanford stable, a new search in the block.
Yebol's mission is to build human-like world's knowledge base and provide knowledge based search (semantics) and services.

Yebol utilizes a combination of patented algorithms paired with human knowledge to build a Web directory for each query and each user. Instead of the common “listing” of Web search queries, Yebol automatically clusters and categorizes search terms, Web sites, pages and contents.

Yebol allows for a multi-dimensional search result instead of the normal one-dimensional search seen by most web search engines today. This provides a more accurate summary of top sites and categories; a wider array of related search terms; a longer and richer expansion for query results; and a deeper base of links and keywords in search result pages.

Unlike current search platforms, Yebol provides hundreds of easily identified and accessibly categorized results in one easily navigable page. The results not only provide users with a rich search experience, but also help them quickly scan the results to find targeted information. In essence, generate a unique “homepage look” for each search query.

Yebol provides a productive experience for both main types of search – general investigation of a topic and specific target search. For users who want to research and explore a topic, Yebol provides rich information from several dimensions. For users who want a specific type of targeted results, they can quickly focus on their category and navigate to the target.

A search for APOE, top most hit (first) gave a expanded definition Apolipoprotein E - on Wikipedia. Followed by link to GHR, wikigenes, gene cards, AD genetics fact sheet form NIA.

It also gives live context sensitive Twitter streaming too.

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.

Thursday, August 6, 2009

BioFocus, Oncodesign Strike Partnership

BioFocus DPI has partnered with the cancer drug candidate and biomarker company Oncodesign to offer an integrated service platform, Galapagos division BioFocus DPI said today.

The agreement will create a service that combines BioFocus DPI's target discovery and screening capabilities with Oncodesign's biomarker and pharmacological services to offer target validation and clinical candidate selection services, the company said.

BioFocus DPI offers gene-to-drug candidate discovery services, including in vitro and cell-based screening, chemogenomic and informatics offerings, storage, distribution, and other structural biology and medicinal chemistry services.

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.

Wednesday, August 5, 2009

XTractor Premium surpasses 200,000 mark of Expert Annotated PubMed Facts

Indian Life Sciences Informatics Company, Molecular Connections announced today, that their XTractor Premium platform surpasses 200,000 "Expert" annotated facts from PubMed.

XTractor Premium – is a platform for discovery, analysis and modeling of published biomedical facts. The application also comes with - XTractor Premium Knowledgebase - the only knowledgebase, which provides "Expert" annotated facts from PubMed on a daily basis. The XTractor Premium Knowledgebase now has more than 202,847 relationships on proteins, drugs, biological process and diseases and is ever growing with more than 600 relationships being added every single day. XTractor provides manually categorized updates on the latest published facts from PubMed for more than 20 categories which include : Biomarkers, clinical trials, dosage, pathways, toxicology, RNAi studies, mutations, knockouts, diseases mechanisms, protein- drug relationships and much more.

Expert Annotated Facts make XTractor Premium a High Quality Knowledgebase and the vast coverage of all biological entities wrapped with in intuitive and analytical software allows researchers more time for science and eliminates the need to consult BioIT experts.

The entities are out linked to over 30 different public databases such as patent databases, wikipedia, clinical trials, and other protein/drug databases.

With XTractor Premium one can,

· Quickly access relevant, high quality expert annotated biomedical facts

· Understand multiple target preferences for a specific drug

· Track common gene polymorphisms across multiple diseases

· Understand Pharmacologic actions, protein interactions and toxicity studies of drugs

And for more, please visit the case study section.

About XTractor Premium

The Knowledgebase: XTractor knowledgebase currently contains 202,847 relationships on biomarkers, clinical trials, pathways, knockout studies, mutations, drug interactions, toxicity, pharmacokinetics, disease mechanisms. It is the Only Knowledgebase that gets updated everyday with manually annotated relationships from the latest PubMed publications and contains more than 856 Unique Drugs, 2569 Unique Diseases, 9286 Unique Proteins, and 2102 Unique Biological Processes. Hence in no time one gets to access one of the largest and the most current manually annotated datasets across the world.

To know more about the advantages of the XTractor Premium and to register for a free trial account and a webex demo please visit XTractor Premium portal

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.

Saturday, August 1, 2009

List of Cheminformatics Companies & Institutions

Also check out these:

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.

Life Science and Informatics

What is this?
is this a new industry?
or a old wine in a new bottle?

Well Life Sciences and Informatics can be anything form computational biology, all omes and omics, core bioinformatics to curation and literature mining, database creation, in the area of biology, chemistry , bio-chem space.

There are number of companies in India and bangalore is the forefront as a major bio-cluster with 20 to 30 companies in this sphere.

now how good are these companies doing?
how good are they in terms of the international markets and how profitable is their business?
what do they do?
their clients?

These are some interesting things that could be discussed in this blog page...

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