Microbial Genomes Curator @ Computercraft Corporation--Maryland (US)

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
* Experience in genome sequencing and annotation
* Familiarity with BLAST, genome browser, and genome assembly data
* Excellent verbal and written communication skills as well as organizational skills
* Strong interest in contributing to the development of public database resources

PREFERENCES:
Other Desirable Skills:
* Programming experience with LINUX/UNIX
* Scripting experience in PERL or related scripting languages

COMPENSATION:
Computercraft offers a competitive salary and an excellent benefits package including PPO health insurance with 100% company paid premiums, 401K program with matching, paid time off and holiday pay, life insurance, flexible spending and disability coverage. We offer an excellent work life balance with a standard 40 hour work week and the chance to work alongside accomplished scientists at NIH/NCBI.

HOW TO APPLY:
To apply for this position or learn about other Computercraft job opportunities, please visit the Careers section of our website: http://www.computercraft-usa.com/

POLICY:
Computercraft is an equal opportunity employer.

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

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?

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.

• The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis
  
• Innovative Features like Semantic Search, Concept Linking, Bibliographic search, Save, Export and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at an Special Introductory Offer. Subscribe now and save!
  
• Request for a Trial
  

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 www.xtractor.in/premium.

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

• The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis
  
• Innovative Features like Semantic Search, Concept Linking, Bibliographic search, Save, Export and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at an Special Introductory Offer. Subscribe now and save!
  
• Request for a Trial
  

XTractor Premium for scientists to access data stored in PubMed says Knowledgespeak

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 annotated relationships from the latest PUBMED publications. Other premium features include semantic search functionality; concept linking; bibliographic search; and the option to save and export data in user-friendly formats.

The XTractor Premium Knowledgebase surpasses 150000 mark

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.

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

• The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis
  
• Innovative Features like Semantic Search, Concept Linking, Bibliographic search, Save, Export and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at Introductory Offer of $450 for Academic Researchers. Subscribe now and save $300!
  
• Register for WebEx
  
• Request for a Trial
  
  

Tracking common gene polymorphisms across multiple Diseases with XTractor Premium

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

• The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis
  
• Innovative Features like Semantic Search, Concept Linking, Bibliographic search, Save, Export and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at Introductory Offer of $450 for Academic Researchers. Subscribe now and save $300!
  
• Register for WebEx
  
• Request for a Trial
  
  

Molecular Connections Launches XTractor Premium for Effective Knowledge Management and real time access to Biomedical data

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 XTractor knowledgebase of 120600 relationships on proteins, drugs, biological process and diseases (which is ever growing). On an average more than 600 manually annotated facts get added to XTractor everyday, thus it is the ONLY Knowledgebase that gets updated everyday with manually annotated relationships from the latest PUBMED publications. 733 Unique Drugs, 2254 Unique Diseases, 7626 Unique Proteins, 1449 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.

Semantic Search Features: The first of its kind highly advanced search feature, where in one could query the XTractor Knowledgebase using multiple ontologies. This would enable one to narrow down on the targets at ease.

Concept Linking: Construct hypothesis from multiple abstracts and discover new facts and relationships, which are hitherto not easily decipherable.

Bibliographic search: Would also enable one to search based on author, organization or country.

Save, Export and Visualize: Provides the utility to save and export data in user-friendly formats. Integration with CytoScape provides better knowledge representation and visualization.

All these Premium Features are available via four licensing options; Academic, Commercial, Governmental and Onsite Installation. XTractor Premium is now available with an Attractive Introductory Offer for Academic Researchers. Subscribe now and save! Visit www.xtractor.in/premium for more details.

Currently, XTractor’s user base includes Abbott, AstraZeneca, Bayerhealthcare, Celera, Cephalon, GSK, JNJ, Novartis, Pfizer, P&G, Wyeth, Vertex, USFDA, NIH, NCI, MD Anderson, Harvard Medical School, Max Planck, Scripps Inst. and many more.

About XTractor Premium

XTractor Premium, a platform for discovery, analysis and modeling of published biomedical facts. The application also comes with XTractor Premium Knowledgebase, the only knowledgebase, which provides "manually" annotated facts from PubMed on a weekly basis.

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 www.xtractor.in/premium.

About Molecular Connections

Molecular Connections is a pioneering In silico Discovery Services Company. It provides high quality, cost effective curation, literature informatics solutions and annotation services as well as products. Dr. Limsoon Wong is the Chairman of Molecular Connections. Customers of Molecular Connections include leading pharmaceutical and biotechnology, drug discovery, genomics, proteomics, medical technology, equipment companies and academic institutions spanning across the globe. In addition, Molecular Connections has powerful tool development, database integration, effective data visualization capabilities, specific expertise in building knowledge bases for rapidly growing needs in, ADME Tox, clinical, drugs, chemistry and patent industries. For more information write to us at xtractorpremium@molecularconnections.comThis e-mail address is being protected from spam bots, you need JavaScript enabled to view it

Recent Awards

Deloitte Technology Fast 50 India Winners |Deloitte Technology Fast 500 APEC Winners |CNBC - ICICI Emerging India Awards ‘Small Enterprise of the Year’

Taming the Data Stampede with Wikis

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 the ability to Share and collaborate
  
  

Sign up it's free, and takes less than a minute. Just click here:www.xtractor.in.

Putting That Bioinformatics 101 Class to Work

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 Beagle Project. Jonathan Eisen's a fan of the work, too, not only because it was metagenomics and published in a PLoS journal, but also because the software is open source.

Pascal Hingamp et al discuss in detail the Open Source, Open Science system for metagenome annotation (see PLoS Biology - Metagenome Annotation Using a Distributed Grid of Undergraduate Students).

They do this as part of a course on metagenome annotation. And the software for running this is all Open Source and available. They say in a way this is a metagenomics version of the Undergraduate Genomics Research Initiative (UGRI) which was described in a PLoS Biology paper previously.

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 collaborate.

Sign up it's free, and takes less than a minute. Just click here:www.xtractor.in.

Does your everyday research constantly demand answers to such questions?

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 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 collaborate.

Sign up it's free, and takes less than a minute. Just click here:www.xtractor.in.

Scientists - Get Networked

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 arrange collaborations with them.

3. The Nature Network. As you might expect, this is the grand-daddy of science social networks. Not only can you set up a contact network, but you can also browse niche-specific forums and groups, start your own blog, and much more.

4. LinkedIn is a site professional networking site for all professions. Unlike the science-specific networking sites,your LinkIn contact list can contain contacts who are not scientists, which is useful if you actually know people in the real world too and it has a more professional atmosphere than Facebook so people of all ages are more likely to join up.

5. Labmeeting primarily allows you to archive, track and share your literature. From your account you can search for papers of interest and upload the PDFs to your account for later retreival. You can also set up streams to keep you informed of the latest publications in your fields of interest, which you can then add to your archive. However, you can also set up a group area to share papers and talk about your interests, and to schedule events, such as lab meetings.

6. XTractor This free service helps discovering newer scientific relations across abstracts. it provides manually curated and annotated sentences for the keywords of your choice. Maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies. Just play around with their drug, disease, etc entity types and you can actually track a drug or process across various diseases across abstracts :)

What social networking sites do you use?

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 collaborate.

Sign up it's free, and takes less than a minute. Just click here:www.xtractor.in.

EBI-Led Consortium to Study How to Turn EU Bio-Databases Into Bioinformatic Network

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 infrastructure itself, promoting database interoperability, and using distributed annotation technologies.

ELIXIR will not unfold with “a big bang” but rather evolve in stages. And it does not solely concern the lions of the European database world such as EBI and the Swiss Institute of Bioinformatics, said Thornton. There are internationally collaboratively maintained databases such as InterPro and IntAct, and also many small ones.

According to Thornton, of the world’s approximately 900 biomedical databases, 40 percent are in Europe, many of which are specialist databases. “They are often in an individual’s laboratory; a research group may have developed a data resource that other people begin to use, and we really need to find a way to incorporate those data resources into the larger network in a way that people can access them easily and without necessarily knowing that they were there in the first place,” she said.

ELIXIR will help link the core and the specialist resources more closely while remaining as “seamless and transparent as possible to our users,” said Thornton. Clicking through databases from link to link is possible for researchers, she said, but clickthrough gymnastics becomes an impossible exercise when a microarray delivers a list of hundreds of genes that must be analyzed with a systems perspective, requiring data to be plowed and mined that is stored in different ways with differing vocabularies.