Bio Saga Blog - A Chronicle of Life Sciences & Informatics

3 Days National Level Workshop on "NGS Data Analysis:Variant Calling,RNASEQ,CHIPSEQ"' 8th to 10th March 2019 09:30 AM - 05:00 PM Topics Covered ▪ Introduction to Bioinformatics ▪ Data curation using Biological databases ▪ Understanding the concept of Gene Expression & Genome Editing ▪ Gene Finding Tools ▪ Introduction to Next Generation Sequencing ▪ Searching for SRA Data for genomic samples ▪ Introduction to Sequence alignment, BLAST ▪ Variant Calling to detect mutations ▪ RNA sample studies for gene expression ▪ Introduction to ChIP-Seq technology Our 3 days comprehensive Workshop on Next Generation Sequencing Data Analysis,Variant Calling, RNAseq, ChIPseq : A Practical Introduction aims at providing systematic Hands-on-Training on using Data Analysis application/tools for the NGS data. This workshop had been conceptualized by eminent scientist having substantial experience in the field of Data Analysis. ...

Qiagen has purchased the assets of Biobase, a Wolfenbüttel, Germany-based provider of curated biological databases, for an undisclosed sum. Qiagen said that Biobase will be renamed Qiagen Wolfenbüttel. Also, Michael Tysiak, BioBase's CEO, will join Qiagen as general manager of the newly purchased company. Founded in 2007, Biobase provides access to curated data assembled by subject matter experts and organized in an accessible and easy to search manner. Its databases support projects focused on functional and gene regulation analyses, variant annotation, pharmacogenetics-based analysis, and more. Among its repositories are the Human Gene Mutation Database (HGMD), which offers access to information on inherited disease mutations; GenomeTrac, which contains data on pathogenic variants; the PharmacoGenomic Mutation Database, which serves as a resource for locating variants that affect drug response; and the Transcription Factor Binding Sites database, which contains information o...

(EMBL-EBI seeking to recruit an enthusiastic Scientific Database Curator to join the InterPro team at the The European Bioinformatics Institute (EMBL-EBI) located on the Wellcome Trust Genome Campus near Cambridge in the UK. The post-holder will work as part of a small team maintaining and curating the InterPro database. Their responsibilities will include updating existing InterPro entries, integrating new predictive signatures and adding annotation such as concise, literature-referenced abstracts. Data in InterPro needs to be of a consistently high quality and so potential candidates should have a good attention to detail and a thorough attitude to their work. We believe that understanding our users' needs and providing for them is critically important, and so the curator may be required to attend conferences, workshops or training events in order to meet with users, hear their ideas and expectations, and teach them about InterPro. The EBI, part of the European Molecular ...

Computercraft seeks a highly motivated Molecular Biologist to join the Gene Expression Omnibus (GEO) curation team onsite at the National Institutes of Health (NIH) in Bethesda, MD. GEO is the largest fully public repository for functional genomic data, primarily microarray and next-generation sequence datasets. More information on GEO can be found on the web site http://www.ncbi.nlm.nih.gov/geo . RESPONSIBILITIES: We are currently looking for someone with a background in molecular biology , genomics, or biomedicine that is capable of working with large datasets. This person will be a member of the GEO curation team, helping to review and process incoming data submissions. The successful candidate will work at NIH's National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM). The successful candidate will perform the following tasks: - Review and evaluate data submissions for structural integrity and content. - Communicate extensively with rese...

"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 ...

Biomedical Data mining happens to be a long-standing problem in scientific research. Scientists are constantly in search of newer and innovative means to mine biomedical data. 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 of preference from time to time, with changing research needs. The categorized sentences could then be tagged and shared across multiple users. Thus XTractor proves to be a platform for getting real-time highly accurate data along with the ability to Share and ...

Blogging about curation in the past several issues have been discussed but here is something very critical. To thrive, the field that links biologists and their data urgently needs structure, recognition and support. Biocuration , the activity of organizing, representing and making biological information accessible to both humans and computers, has become an essential part of biological discovery and biomedical research. But curation increasingly lags behind data generation in funding, development and recognition. Three urgent actions to advance this key field. First, authors, journals and curators should immediately begin to work together to facilitate the exchange of data between journal publications and databases. Second, in the next five years, curators, researchers and university administrations should develop an accepted recognition structure to facilitate community-based curation efforts . Third, curators, researchers, academic institutions and funding agencies should, in the ...

XTractor now has over Over 150 registered users from FDA , NIH , NCI , Astra Zeneca , Wyeth , MD Anderson Cancer Institute , Washington university , Scripps institute , Max Planck , Harvard Medical school and many more in less than 3 weeks !!! More than 600 annotated facts added everyday. A total of 25,000 facts added till date!!! 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 of preference from time to time, with changing research needs. The categorized sentences could the...

Molecular Connections , a life sciences informatics major, is now looking at acquiring small and medium-sized companies as part of its inorganic growth strategy. "The acquisition will depend on good technology fit and domain expertise that could plug into our products and services,'' Jignesh Bhate, CEO, Molecular Connections Pvt Ltd told Pharmabiz . "We are aggressively scouting for companies both in India and abroad. If we lay our hands on an international company, we will have access to their customers. In the case of an Indian company, we are essentially looking at a synergy in content and database,'' Bhate said. To facilitate these acquisitions, Molecular Connections has identified three options to raise funds: internal accruals, foreign loans and venture funds. The mode of raising capital will depend on the size of the deal and the company is in talks with foreign banks. Around $2 million was raised from Barings Private Equity in 2006 for expansion. Early...

The first of its kind - SCIENTIFIC LITERATURE alert service which also provides manually annotated sentences for the keywords of YOUR preference Highly accurate , manually annotated sentences for given keywords. Daily scientific literature updates at your desktop along with extracted facts - manually curated. Provision to change keywords with your changing research preferences. Annotated sentences and abstracts get stored in your profile, as and when they get updated in PubMed. Classify and create your own datasets of annotated facts. Enhanced experiences of reading & analyzing literature. Access your profile / datasets from anytime, anywhere. Discover and Create newer relations from scientific facts classified by the XTractor™ Community. Tag your favorite abstracts and share them across other users. Much more faster and an Absolutely Free Service PRODUCT HIGHLIGHTS Abstract Summarization The XTractor™ system would provide extracted relations in addition to id...

Already blogging on similar lines and the subject of Bring in data from the published literature in my earlier blog Smart tools to track, analyze and visualize research , here is another interesting experiment on similar lines: The experiment centres on Structured Digital Abstracts (SDA). SDA are extensions of the normal journal article abstracts that describe the relationship between two biological entities , mentioning the method used to study the relationship. Each sentence is preceded by one or more identifiers pointing to the corresponding database entries that contain the full details of the interaction e.g. protein A interacts with protein B, by method X . The aim of SDA is to assist data entry, text mining and literature searching by extracting the salient data from the article into simple sentences using a defined structure and controlled vocabularies. Gianni Cesareni, Editor of FEBS Letters explains: Many articles in biological journals describe relationships between ent...

The Single Nucleotide Polymorphisms database (dbSNP) serves as a central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Computercraft seeks a biologist with significant knowledge in life sciences to help curate dbSNP records, process submission, and perform data analyst tasks. Candidates should also have the ability to rapidly develop applications to process data into database and to generate reports. The individual will work onsite at the National Institutes of Health (NIH) in Bethesda, MD. Our scientists work with genomic experts at NIH's National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM) to create and enhance a suite of databases and tools available to researchers worldwide . Requirements: • PhD or M.S. in molecular biology, bioinformatics, or highly related field • Linux/UNIX experience • Relational database and SQL experience • Programming experience (Perl, Python, or C++) •...

" Work created before the existence of copyright and patent laws also form part of the public domain . The Bible and the inventions of Archimedes are in the public domain. However, copyright may exist in translations or new formulations of this work. " [ Wikipedia ] As posted by Tony is the Chemical Abstract Service (CAS) discouraging using their CAS services for assigning correct CAS numbers to structures for any third party database. Wikipedia is a source of structures, which is public domain due to its GNU FDL . Still, this does not imply that any translation of structures, e.g. CAS numbers, are in the public domain, too. Honestly, this raises a serious problem for curating CAS numbers on Wikipedia and this raises indeed the question, if they should not be dropped from Wikipedia, and any other information source, at all? Is it not better having no information, than having wrong information? A CAS number is for me only one certain translation of a chemical structure....

Yes i am talking about the development in the field of literature search and scientific publication search. Looking beyond NLP some of the advancements and service models based on NLP and other advanced methods. Today to the user's delight there are quite a few companies and organization that provide services that absolutely make an scientist life easy! These services revolve around customized alert services for selected search terms, specific research area of interest even more so pertaining to a list of custom key-word and search terms that the service providers allow the user to choose form. The scientist can simply subscribe to such service, sit back and wait for daily updates. The updates are provided on a day to day basis at his desktop. He gets abstract summarization , full text summarization so that he need not actually go through the ordeal of reading through pages of scientific literature. Some once else does the job for him and just pick up the right things that he woul...

What is this? is this a new industry? or a old wine in a new bottle? may be the later is true, bioinformatics is more popularly known by this name in the industry circle these days! Well Life Sciences and Informatics can be any thing form 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. Cheminformatics , insilico chemistry and insilico biology how best to describe the host of activities involved that companies do to serve their clients and earn revenues for their firms... There are number of companies in India and bangalore is the forefront as a major bio-cluster with 20 to 30 companies operation in this sphere. there are companies with the sole focus as informatics as business to name a few : Molecular Connections Pvt. Ltd. Jubilant Biosys Strand Life Sciences Ocimumbio (hyderbad) While IT companies which are also in to Life Sciences as one of thei...