Bio Saga Blog - A Chronicle of Life Sciences & Informatics

Wow this an interesting article enjoy it! With the increasing ubiquity of smartphones, the growing popularity of tablets, and the burgeoning market for third-party applications, the public appetite for touchscreen technology is virtually impossible to ignore. It shouldn't, then, surprise anyone that bioinformatics software developers would look for ways to tap into the multi-touch market. But it's not just about making sure that download tallies are going up. In fact, some life science application developers say they dipped into the app space out of sheer curiosity more than anything else.   "For us, it was an experiment," says Andrew Su, an associate professor at the Scripps Research Institute. His laboratory developed an application called BioGPS, a mobile version of his group's web-based gene annotation portal, which runs on Apple's iPhone. "We imagined that somebody in a meeting or a seminar or at a conference who needed quick access to ...

Microbial Genomes Curator @ Computercraft Corporation--Maryland (US).  Submitted by Computercraft Corporation; posted on Saturday, March 17, 2012 RESPONSIBILITIES: Computercraft seeks a microbiologist to work with a team of software developers and biologists on microbial genome analysis including pan-genome, protein clusters, phylogenetic tree and more. This is a technically challenging position requiring experience in genome sequencing and annotation. A background in comparative genome analysis such as alignments and tree building is a plus. Our scientists work with genomic experts at the NIH's National Center for Biotechnology Information (NCBI) to create and enhance a suite of databases and tools available to researchers worldwide. Teamwork interaction and excellent organizational skills are essential for this detail-oriented position, as is scientific problem-solving with a results-oriented focus. REQUIREMENTS: * PhD in molecular biology, microbiology, or related field * ...

Pathway analysis has become the first choice for gaining insight into the underlying biology of differentially expressed genes and proteins, as it reduces complexity and has increased explanatory power. We discuss the evolution of knowledge base–driven pathway analysis over its first decade, distinctly divided into three generations. We also discuss the limitations that are specific to each generation, and how they are addressed by successive generations of methods. We identify a number of annotation challenges that must be addressed to enable development of the next generation of pathway analysis methods. Furthermore, we identify a number of methodological challenges that the next generation of methods must tackle to take advantage of the technological advances in genomics and proteomics in order to improve specificity, sensitivity, and relevance of pathway analysis. Do you wish to know more?

"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 ...

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 Pr...

Life sciences informatics company Molecular Connections , India, has announced the availability of XTractor Premium, a knowledge management platform, for the biomedical research community. The product is projected to provide scientists with new and refined ways to access the latest scientific facts from PubMed. Pharmaceutical companies, researchers and scientists can use the platform to identify, verify and develop predictive relationships from PubMed Literature. Leveraging the ability to transform data to knowledge and to assist experts is seen to be crucial to the success of research investigation today. XTractor Premium offers several enhancements over the beta version in managing large volume of published biomedical data to accelerate decision making. The XTractor knowledgebase currently contains 150,000 relationships on biomarkers, clinical trials, pathways, knockout studies, mutations, drug interactions and disease mechanisms. The knowledgebase is updated everyday with manually a...

XTractor Premium - a platform for discovery, analysis and modelling of published biomedical facts. The application also comes with -XTractor Premium Knowledgebase - the only knowledgebase, which provides "manually" annotated facts from PubMed on a daily basis.The XTractor Premium Knowledgebase now has more than 150000 relationships. TAGS: text mining, manual annotation, data alerts, pubmed, genes, drugs, processes, diseases, free, data mining, tag, drug discovery, web 2.0, natural language processing, data analysis, visualization, concept linking, abstraction, precision, recall, data accuracy, proteins, interactions, index, query, MeSH, NLM, manual curation, protein interactions, abstraction, abstracts, accuracy, accurate, data, annotations, biological process, biomedical literature, categorization, colloborations, concept linking, curate, curation, data accuracy, data alerts, literature, categorization, colloborations, concept linking curate curation data accuracy data ale...

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Bangalore, India — Indian Life Sciences Informatics Company, Molecular Connections announced today, the launch of XTractor Premium ( www.xtractor.in/premium ), a new Knowledge Management Platform designed to enable Pharmaceutical Companies, Researchers, Scientists identify, verify and develop predictive relationships from PubMed Literature. “ The release of XTractor Premium reflects the evolution of our client’s knowledge management needs and our continued commitment to provide knowledge solutions which add value & bring better efficiencies in Drug discovery,” said Jignesh Bhate CEO Molecular Connections. Leveraging the ability to transform DATA to KNOWLEDGE to assist experts is crucial to the success of drug development today. XTractor Premium offers several enhancements over the beta version in managing large volume of published biomedical data to accelerate decision making in drug discovery. Data Search: One would be able to perform searches over the entire XTra...

Well, the creation and use of Wikis can help scientists to lasso the stampede of new genomic and proteomic data and corral it into useful knowledge rather than just random facts and figures running wild on the open frontier of the Internet. Be part of XTractor community. XTractor the first of its kind - Literature alert service , provides manually curated & annotated sentences for the Keywords of your choice XTractor maps, extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies Enables customized report generation. With XTractor the sentences are categorized into biologically significant relationships The categorized sentences could then be tagged and shared across multiple users Provides users with the ability to create his own database for a set of Key terms Users could change the Keywords of preference from time to time, with changing research needs XTractor thus proves to be a platform for getting real-time highly accurate data along with th...

In a paper called "Metagenome Annotation Using a Distributed Grid of Undergraduate Students" I just love this title! It's nerdy and cute, all at the same time. Says Sandra Porter . The paper describes a class where students from Marseilles University investigate the function of unidentified genes from a Global Ocean Sampling experiment. All the sequences are obtained from the environmental sequence division at the NCBI . French researchers describe their strategy for teaching undergraduate-level bioinformatics using cutting-edge genomic data and a Web-based learning tool. The students then annotated real metagenomic sequences from the Global Ocean Sampling experiment. "In return for their much-needed help sorting out oodles of DNA data, the undergrads gain a practical knowledge of the work involved in doing bioinformatics and metagenomics, and, most importantly of all, they get to experience what it's like to do real research," says Karen James at the Be...

Ask XTractor - XTractor™ now turns ON its ‘Insta Search’. Get a snapshot of the XTractor data for your desired query using the Insta Search feature. Which are the biological processes involved in Leukemia? What are the drugs associated with Ovarian Neoplasm? What are the diseases modulated by FRAP? Then get a snapshot of the XTractor data from the latest published abstracts on your questions using the 'Insta Search' feature. Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into biological significant relationships and it also provides the user with the ability to create his own database for a set of Key terms. Also the user could change the Keywords...

Social networking is the latest buzz on the internet. You’ve heard about it, but what does it mean to you as a scientist? Well for one thing, it means that networking has never been easier. Here are six of the best social networking sites for scientists that are designed to help you make and maintain your professional contacts. 1. SciLink is a souped-up networking site that actually knows who a lot of your contacts will be before you even sign up. Uniquely, SciLink mines literature databases to build a network of professional relationships that you can slot into (and of course expand further) when you sign up. You can also find jobs, discussion, news etc on the site. 2. MyNetResearch is a powerful website for finding collaborators for your project. You set up your own account/profile and build a network of contacts as with the other social networks but MyNetResearch is designed to help you find people who work in the areas you are interested in (or interested in expanding into) and ...

The European Commission has awarded €4.5 million ($7 million) to a consortium of 32 research organizations, universities, and companies from 13 countries to determine how to transform Europe’s biomedical data resources into a transnational “sustainable integrative bioinformatics network” for the life sciences. The consortium is led by the European Bioinformatics Institute. The first year and a half of this project, called ELIXIR, for European Life-science Infrastructure for Biological Information, is aimed at gathering input, performing technical-feasibility studies, and doing user surveys among researchers who generate and use data, and develop tools. Much like the Oxford English Dictionary, which will remain useful as long as people speak English, so, too, will “the infrastructure for biological information … continue as long as people are interested in biology, health, and medicine,” she said. But provisions must be made to allow that to happen, including upgrading the infrast...