Database Curator@EBI for InterPro database

(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 Biology Laboratory (EMBL), provides cutting-edge research, services and training in the field of bioinformatics and is home to world-class resources such as UniProtKB and InterPro. InterPro generates and houses data predicting the functional classification of protein sequences and the presence of protein domains and sites. This information is widely used by genome sequencing projects and is disseminated to a large, global biological research community through web-based databases and software tools.

Requirements: 

The ideal applicant should hold at minimum a BSc. in a Biological Science, preferably with a strong background (e.g. 3 years post-graduate experience) in proteomics, molecular biology, biochemistry, cell biology and/or a related field.

Past work must either include work in a laboratory or in a biological database environment. A good understanding of proteomics and protein evolution would be advantageous, as would a high standard of scientific writing, with experience writing specifically for the web. Familiarity with the use of software tools for nucleotide/amino acid sequence analysis would be an advantage. The role is part of a tightly-knit team, so an ability to communicate ideas and openly discuss potential approaches will be very important. However, applicants should also be able to take their own initiative and work autonomously.

The candidate may be required to describe their work to a wider audience, including end-users of the database, so good presentation skills and an ability to write training materials and teach are a necessity; some of their work may also be published in scientific journals.

No computer programming skills are necessary but a proficiency at using Microsoft Office and a willingness to learn how to use new software tools are a must.

Contact Information: 

http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jj&id=48329&aid=15470

About Our Organization: 

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation.

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

Note that special visa requirements apply to employees from non EU countries working at EMBL-EBI in the UK. The period of work does not qualify for the Highly Skilled Migrants Programme.

Online Linux course for biologists

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                    CS101F Linux for Biologists, Level 1
                              Jan. 24-26, 2012
                        Online at Bioinformatics.Org

                    http://www.bioinformatics.org/edu/ACGG

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OBJECTIVES:
This course teaches biologists how to use the powerful Linux operating system to work with biological data.

No programming experience is needed, just a need to utilize Linux for biological research.

INSTRUCTOR:
Shailender Nagpal is a data analysis consultant in the biotechnology and pharmaceutical industries and specializes in the interpretation of data generated from various platforms in drug discovery, such as genomics and proteomics.

SYLLABUS:
Session 1: Fundamentals of the Linux OS - filesystem, access and basic commands; navigation of the filesystem and basic file operations - reading, writing, merging, copying and moving

Session 2: Setting permissions of files and directories; file manipulations using awk and sed, file redirection and piping, command line execution of various bioinformatics programs; exercise to demonstrate getting data and software from the internet and crunching through some real data generated from experiment; shell scripting basics and an example of a bioinformatics workflow implemented with unix shell programming

Homework assignments will involve running commands learned in the live lectures.

SCHEDULE:
The lecture is scheduled for 12:00 noon to 1:00 PM US EDT (17:00 to 18:00 GMT), Tuesday and Thursday. It will also be recorded for later viewing. 

REGISTRATION:
If you haven't already done so, create an on-line account to access the educational section of our website. Register for the course by making a payment using the on-line registration form (use this form only for PayPal payments and credit card payments via secured PayPal):http://www.bioinformatics.org/edu/ACCT.

For additional payment methods, please write to edu@bioinformatics.org.

Tuition:
* For-profit & government: $400 USD
* Non-profit & self-pay: $200 USD

Additional discounts are available as follows:
* Professional Members: 20% discount
* Limited scholarships may also be available for those residing in low-income economies (please inquire).

FOR MORE INFORMATION:
Please visit http://www.bioinformatics.org/wiki/CS101F or write to edu@bioinformatics.org.

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.

YEBOL 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.

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Search Wars

A not very long time ago, in a galaxy near,
very near by....

SEARCH
WARS

Search, Search engines, While the Search engine big wigs fight for a niche in the search engines landscape .... The Google, Yahoo & now Micorsoft too (with their Bing)

There are the Wolfram|Alpha likes that are forming a separatist and slowly gaining power over the Google order. In fact google has managed to bring balance to both with its Google Squared.

While platforms like XTractor, NextBio, Novoseek, GoPubMed, BioMedSearch have specialized in searching biomedical and biological knowledge are even more strengthening the separatists.

Now to see and know who is more powerful, the galactic empire or the separatist? I leave it to the 'Republic' i.e. You users! to judge, in the form of your comments and experiences with such tools and searches! you could even voice your opinions here

Anna University develops bio-defence shield

Microbes as bio-defence against chemical weapons, a skin-thin membrane to protect soldiers against toxic environments and cost-effective bio-diesel to fuel military vehicles are among the contributions researchers in the city are set to make for the Indian solider. Developing these futuristic systems is Anna University, with funding from the Defence Research and Development Organisation (DRDO).

Of the 12 projects the university submitted, DRDO has approved four and allocated Rs 88 lakh as the first instalment. "The projects are research for bio-defence against pathogens and toxins, development of membranes for gas and organic vapour separation, development of novel anti-fouling nano and ultra filtration membranes (these membranes will prevent the solider from imbibing nano-sized toxins) and development of alternative source for bio-diesel from non-edible oils," D Mohan, a senior scientist with Anna University told the press.

The most important among these is the research on development of bio-defence. "The threat of biological warfare is real, as enemies can unleash bacterial and viral pathogens resistant to known drugs. Even while trying to develop drugs against these pathogens, we have to develop new categories of probiotic microbes, considered good microbes, to resist and overpower toxic microbes,' said K Sankaran, a biotechnologist involved in the project, said.

He added that research is on to develop prevention systems. "We are developing sophisticated remote sensing systems to identify the probable nature and signature of the toxins that the enemies could use. We are also looking at microbes which could be used to negate the effects of a biological attack."

An effective mask against such toxic materials would be a membrane under development that can keep out noxious gases from inhalable air. "This membrane will be used in gas masks. Our challenge is to allow oxygen in and keep harmful and organic vapours out. We have the expertise in membrane technology and we hope to successfully complete the project soon," D Mohan said.

The team developing the membrane is also involved in the research on anti-fouling nano and ultra filtration membranes. "Bio-fouling, the formation of a mucous-like membrane over objects kept in water for long duration, is the main reason for damage of membranes in treatment plants. We need to develop a membrane which can prevent bio-fouling and can perform consistently. Our soldiers, who are camping in extreme conditions, do not get good quality drinking water. With the development of these membranes, the efficiency of water treatment plants in extreme condition will improve," Mohan said.

Anna University is also developing cost-effective bio-diesel from non-edible oil. The aim of this research is to bring down the cost of fueling military vehicles.

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An ontology that bridge biological and computational spheres in bioinformatics

IMGT®, the international ImMunoGeneTics information system (http://imgt.cines.fr), is the reference in immunogenetics and immunoinformatics. IMGT standardizes and manages the complex immunogenetic data that include the immunoglobulins (IG) or antibodies, the T cell receptors (TR), the major histocompatibility complex (MHC) and the related proteins of the immune system (RPI), which belong to the immunoglobulin superfamily (IgSF) and the MHC superfamily (MhcSF). The accuracy and consistency of IMGT data and the coherence between the different IMGT components (databases, tools and Web resources) are based on IMGT-ONTOLOGY, the first ontology for immunogenetics and immunoinformatics.

IMGT-ONTOLOGY manages the immunogenetics knowledge through diverse facets relying on seven axioms, ‘IDENTIFICATION’, ‘DESCRIPTION’, ‘CLASSIFICATION’, ‘NUMEROTATION’, ‘LOCALIZATION’, ‘ORIENTATION’ and ‘OBTENTION’, that postulate that objects, processes and relations have to be identified, described, classified, numerotated, localized, orientated, and that the way they are obtained has to be determined. These axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope.

These axioms have been essential for the conceptualization of the molecular immunogenetics knowledge and for the creation of IMGT. Indeed all the components of the IMGT integrated system have been developed, based on standardized concepts and relations, thus allowing IMGT to bridge biological and computational spheres in bioinformatics. The same axioms can be used to generate concepts for multi-scale level approaches at the molecule, cell, tissue, organ, organism or population level, emphasizing the generalization of the application domain. In that way the Formal IMGT-ONTOLOGY represents a paradigm for the elaboration of ontologies in system biology.

for more

"Modern bio-science is incredibly interdisciplinary now," Thanks-The life sciences are thriving

There was a time when bio-science was the Cinderella science: meticulous, certainly, and worthwhile, but far from glamorous. All that changed in 2003, when the sequencing of the human genome was completed.

Now masses of data and the potential for radical technologies are attracting the best graduates in chemistry, physics, engineering and maths. And bio-science offers more than intellectual curiosity, explains Professor Sir David Read, Biological Secretary and Vice-President of the Royal Society. "It's the human factor," he says. "Cross-disciplinary approaches are addressing many of the major threats to humanity: disease prevalence, antibiotic-resistant micro-organisms, avian flu, the threats to the environment associated with climate change."

The biological sciences are as varied, and sometimes as confusing, as life itself, taking in such disparate disciplines as neuroscience and taxonomy, environmental science and microbiology, physiology and biochemistry. At Cambridge University alone, there are 21 life-science departments.

What is exciting many dons at the moment is omics, or systems biology, which is allowing study to shift from single genes or proteins to how they work together in biological systems.

"The omics system is producing massive amounts of data that we have trouble finding people to make sense of," says Dr David Sargan, director of graduate education in the life sciences at Cambridge.

Mathematicians, physicists, chemists and engineers are all being brought in. "Modern bio-science is incredibly interdisciplinary now," says Professor Paul Freemont, head of molecular bio-sciences at Imperial College London.

Systems biologists are building mathematical models that simulate the living cell, synthetic biologists are redesigning biological systems, chemical biologists are probing living systems at the chemical level, and physicists and engineers are bringing imaging wizardry to bear in biology, from the molecular to the cellular level.

"The biological sciences are going through a revolution," says Professor Freemont. "It's very exciting in the life sciences right now. Students from other disciplines find it fascinating: they see this wonderful opportunity to develop new strands of science."

Interesting: Do you want to know more?

Videos about Science, Visualization, Research and more

Videos in Biosciences

GenBank celebrates 25 years of service

Leading scientists discuss DNA database at April 7-8 Meeting

For a quarter century, GenBank has helped advance scientific discovery worldwide. Established by the National Institutes of Health (NIH) in 1982, the database of nucleic acid sequences is one of the key tools that scientists use to conduct biomedical and biologic research. Since its creation, GenBank has grown at an exponential rate, doubling in size every 18 months. In celebration of this vital resource and its contribution to science over the last 25 years, the National Center for Biotechnology Information, National Library of Medicine (NLM), NIH, is holding a two-day conference on GenBank.

The conference will take place April 7-8, 2008 at the Natcher Conference Center on the main NIH campus in Bethesda, Maryland. For details on the meeting, see the conference Web site, at http://www.tech-res.com/GenBank25. The conference is open to the public and also will be available via live and archived webcast; the April 7 proceedings can be viewed at http://www.videocast.nih.gov/summary.asp?live=6670 and the April 8 proceedings at http://www.videocast.nih.gov/summary.asp?live=6671.

The conference will bring together a slate of world-renowned scientists in molecular biology, genetics, bioinformatics and other areas to discuss GenBank's applications, the discoveries it has enabled, its history, and future directions. Speakers include Rich Roberts, Ph.D., a Nobel Prize winner for his discoveries of split genes, and currently Chief Scientific Officer at New England BioLabs; Sydney Brenner, Ph.D., a Nobel Prize winner for his work on genetic regulation of organ development and programmed cell death, and currently a professor at the Salk Institute; Francis Collins, M.D., Ph.D., who led the Human Genome Project and is Director of NIH's National Human Genome Research Institute; and Craig Venter, Ph.D., who led the private-sector effort to sequence the human genome and is President of the J. Craig Venter Institute. More than a dozen other eminent scientists will be speaking; the full list of presenters can be viewed at the GenBank conference Web site.

"Each day, researchers across the world submit tens of thousands of sequences to GenBank and collaborating databases in Europe and Japan," said Donald A. B. Lindberg, M.D., Director of the National Library of Medicine. "Because of these contributions, GenBank has become an essential tool for molecular biology. The National Library of Medicine is proud to partner with the research community in making this valuable resource available."

Rich Roberts, Ph।D., Chief Scientific Officer at New England BioLabs, commented, "GenBank has provided a foundation upon which much of contemporary biology is now based. It is becoming almost impossible to conceive of any serious biological study of a new organism that does not begin with the determination of its DNA sequence, which of course must be stored in GenBank." Roberts, one of the early proponents of the database, added, "the availability of this wealth of sequence information in a single repository is something we could only dream about in 1979 at the Rockefeller Conference that led to its creation and which we could not imagine being without today."

for more details