Posts Tagged ‘Bioinformatics’

eXframe Platform Demos Power Of The Semantic Web For Biology

sccommonsA Drupal ++ platform for semantic web biomedical data – that’s how Sudeshna Das describes eXframe, a reusable framework for creating online repositories of genomics experiments. Das – who among other titles is affiliate faculty of the Harvard Stem Cell Institute – is one of the developers of eXframe, which leverages Stéphane Corlosquet’s RDF module for Drupal to produce, index (into an RDF store powered by the ARC2 PHP library) and publish semantic web data in the second generation version of the platform.

“We used the RDF modules to turn eXframe into a semantic web platform,” says Das. “That was key for us because it hid all the complexities of semantic technology.”

One instance of the platform today can be found in the repository for stem cell data as part of the Stem Cell Commons, the Harvard Stem Cell Institute’s community for stem cell bioinformatics. But Das notes the importance of the reusability aspect of the software platform to build genomics repositories that automatically produce Linked Data as well as a SPARQL endpoint, is that it becomes easy to build new repository instances with much less effort. Working off Drupal as its base, eXframe has been customized to support biomedical data and to integrate biomedical ontologies and knowledge bases.

Read more

Bioinformatics Big Data Startup InterpretOmics Raises $1.6M

Anand Rai of Tech Circle reports, “Bangalore-based InterpretOmics India Pvt Ltd, a Big Data startup focused on bioinformatics, has raised Rs 10 crore ($1.6 million) in angel funding from Amarante, a Singapore-based shipping company, and two unnamed Indian investors. The funds will be used for product development, research and marketing. The company was founded in 2009 by Prahalad H. Achutharao (CEO) and Asoke Talukder (chief scientific officer). Achutharao had earlier worked at Infosys, Verari Systems and other companies. He holds an MS degree in Computer Science from the University of Alabama at Birmingham (US) and a BE degree in Electrical Engineering from Karnataka University. Prior to InterpretOmics, Talukder also worked with several companies such as Sobha Renaissance, Tyfone Communications Development India, Cellnext Solutions, Bluestar Infotech and Mindware.” Read more

Semantic Web Jobs: NIH

The National Institutes of Health is looking for a Post Doc candidate in Bioinformatics in Bethesda, MD. The post states, “The Bioinformatics Programmer/Developer/Coder applicant’s Ph.D. degree must be in computer science or mathematics from an accredited university with 3-5 years Post-Doctorial experience in Bioinformatics, Semantic Web and RDF/XML to serialize RDF and OWL ontologies utilizing a primary computer language such as C, C++, C#, Java, Lisp, Python etc. Responsibilities include the development of middle ware for various high-throughput omics data QC analytics, and creating analytical applications that union and intersect geocoding (ArcGIS), omics data, electronic medical records and other clinical data with analytical applications such as R, Bioconductor, MATLAB, and SAS.” Read more

New Paper: Semantic Web meets Integrative Biology

A new paper is available for purchase entitled Semantic Web meets Integrative Biology: A Survey. The paper was written by Huajun Chen, Tong Yu, and Jake Y. Chen. According to the abstract, “Integrative Biology (IB) uses experimental or computational quantitative technologies to characterize biological systems at the molecular, cellular, tissue and population levels. IB typically involves the integration of the data, knowledge and capabilities across disciplinary boundaries in order to solve complex problems.” Read more

Metaome Helps Bench Biologists Get More Value From Linked Data

How to help the bench biologist get value out of the wealth of life sciences Linked Data sets? Startup Metaome Science Informatics proposes to offer some help with its DistilBio semantic search and data integration technology, by streamlining the approach to posing user queries. The Distil in DistilBio stands for Data Integration using Semantic Technologies in the Life Sciences.

Metaome, which was founded by CEO Kalpana Krishnaswami and CTO Ramkumar Nandakumar as a bioinformatics services provider before transitioning to a product vendor, contains a few more than a dozen life sciences public data sets so far. Infomaticians in the life sciences space have the expertise to query such data across sets via SPARQL, but the front-line biologist isn’t necessarily an infomatician. So, DistilBio has created a query interface that makes it easier for them to ask large and complex questions in a simplified way across data sets while building a graph in the process.

“How does a user say what are the drugs used for Alzheimer’s disease and do have they have certain protein targets and are those protein targets implicated in other diseases?” says Krishnaswami. “To ask that in one shot right now is hard without working through a SPARQL endpoint using all the SPARQL syntax.”

Read more

Semantic Web Jobs: Life Technologies

Life Technologies is looking for a Senior Staff Scientist – Bioinformatics in Carlsbad, CA. The post states, “Life Technologies is seeking candidates with a background and experience in bioinformatics software technologies and products design, development and support for molecular biology, genomics and synthetic biology. The candidate will employ expertise in bioinformatics, data analysis, biological insight, and software engineering to bring an engineering perspective to the practice of molecular biology, in order to promote the newly developing field of synthetic biology. The ability to communicate with customers, lead and manage projects, design, test, document, and communicate results to diverse audiences are important aspects of this role.” Read more

Semantic Web Jobs: Stanford & Pfizer

Stanford University is looking for a Web UI and Backend Server Developer in Palo Alto, CA: “Stanford University is the home for a national center to apply advances in computing to improve the effectiveness of biomedical research and health care. The user-facing part of our center is primarily an open-source web portal for collecting, categorizing, and applying medical and biological terminologies in innovative ways (http://bioportal.bioontology.org). In addition, we provide programmatic access to this information to allow others to build upon our technology. One of the applications of this system provides search of biomedical literature and clinical records that is much more effective than has previously been possible.” Read more

Semantic Web Jobs: Life Technologies

Life Technologies is looking for a Staff Scientist of Bioinformatics in Foster City, CA: “We are  seeking to recruit a  computational biologist to contribute to the development of a knowledge discovery environment  to enable genome-based medicine. This individual will develop and apply pathway analysis, semantic technology, and system biology methods and tools to integrate disparate biological knowledge with full genome and transcriptome sequencing data form patient’s germline and cancer tumors genomes. Working closely with customers and collaborators, the candidate will be responsible for developing data mining strategies for inferring disease pathways affected by inherited and somatic genetic variants and alterations.” Read more

Introducing RIKEN

According to a recent article, “A new lightweight web service interface for accessing massive amounts of life science research data across multiple public and private domains has been developed by researchers at RIKEN, Japan’s flagship research institute. Through the powerful RIKEN Scientists’ Networking System (SciNetS), the service provides a secure, flexible and light weight interface to millions of data records and their network of semantic relationships, ushering in a new era of collaboration, analysis and information-sharing for life science research and applied innovation.” Read more

Semantic Web Jobs: Life Technologies

Life Technologies is seeking a Senior Bioinformatic Applications Scientist/Software Developer in Carlsbad, CA: “Life Technologies is seeking candidates with a background and experience in bioinformatics software technologies and products design, development and support for molecular biology, genomics and synthetic biology. The candidate will employ expertise in bioinformatics, data analysis, biological insight, and software engineering to bring an engineering perspective to the practice of molecular biology, in order to promote the newly developing field of synthetic biology.” Read more

NEXT PAGE >>