Post Doctoral Fellow in Wellcome Trust DBT India Alliance project at NII, New Delhi

Applications are invited for the post of Post Doctoral Fellow for the following time-bound sponsored project as per the details given below:

Post : Post Doctoral Fellow

• Consolidated fellowship : As per terms governed by the Wellcome trust DBT India Alliance and National Institute of Immunology (a Minimum of Rs. 40,000/- per month). 
• Project title : Exploring the role of a developmental regulator in inflammatory immune response under Wellcome Trust DBT India Alliance

Essential Qualification : a. Must hold a Ph.D Degree (not awarded before 2009), or must already have submitted their thesis towards obtaining a Ph.D degree from a reputed Institute.
b. Must have more than Five years of research Experience.
c.  Must have proven research expertise/skills in basic biochemistry, cell biology and Molecular Biology, Research Expertise in in vivo animal work is also preferred.
d. Must have one publication as first author, in international journal, preferably with impact factor above 2.5.
e. Must have basic theoretical knowledge in the area such as cell signalling, inflammation, Immunology.

• Job description/Experience : The Candidate is ready to explore alteration in the host cell signalling and transcription network in response to pathogenic perturbations. The Candidate should have sound technical skills in cell culture and biochemistry and should have working theoretical knowledge in cell signalling. The candidate must have a Ph.D Degree (or must have submitted his/her thesis towards obtaining a Ph.D degree) and more than 5 years of experience in research laboratories. 

Duration : 30.11.2015
PI : Dr. Soumen Basak | sobasak@nii.ac.in  

How to Apply :Interested candidates may apply directly, STRICTLY IN THE PRESCRIBED FORMAT GIVEN ON WEBSITE through e-mail, to the Investigator of the project, clearly indicating the name of the project along with their complete C.V., e-mail id, fax numbers, telephone numbers. Short listed candidates will be required to submit attested copies of all their certificates and a Demand Draft of  Rs 100/- drawn on Canara Bank or Indian Bank payable at Delhi / New Delhi in favour of the Director, NII (SC / ST and PH candidates are exempted  subject to submission of documentary proof), at the time of interview.

Deadline : 28.03.12

http://202.54.226.233/announcement/AnnounceIndex_106.html

International Conference on Intelligent Biology and Medicine (ICIBM 2012)

DATES: April 22-24, 2012
LOCALE: Nashville, TN
URL: http://bioinfo.mc.vanderbilt.edu/icibm/index.html

Bioinformatics, Systems Biology and Intelligent Computing are synergistic disciplines that hold great promise for the advancement of biomedical research and development through the design of intelligent systems to solve engineering practical problems as well as translational science problems. Research and development in these areas impact science and technology, and synergies among these disciplines provide enormous potential. The International Conference on Intelligent Biology and Medicine (ICIBM) aims to provide a forum for the cross- fertilization of ideas and promotion of interdisciplinary collaborations.

3rd INTERNATIONAL CONFERENCE on BIOINFORMATICS AND SYSTEMS BIOLOGY

3rd INTERNATIONAL CONFERENCE on BIOINFORMATICS AND SYSTEMS BIOLOGY (INCOBS-2012)

16th -18th February, 2012 ANNOUNCEMENT & CALL FOR PAPER

Organised by DEPARTMENT OF ZOOLOGY(DDE) Annamalai University Annmalainagar-608002 Tamilnadu, India

Do you wish to know more?

4th National Symposium cum Workshop on "Recent Trends in Structural Bioinformatics and Computer Aided Drug Design"

Greetings from Department of Bioinformatics, Alagappa UniversityIt gives us immense pleasure to announce that the Department ofBioinformatics, Alagappa University, Karaikudi is organizing 4thNational Symposium cum Workshop on “Recent Trends in StructuralBioinformatics and Computer Aided Drug Design [SBCADD’2012]” duringFeb 20th – 23rd, 2012. The motive of the National symposium cumworkshop is to provide theoretical and practical exposure ofStructural Bioinformatics and Computer Aided Drug Design amongacademicians and technocrats in order to cater the industrial andacademic need.We have invited eminent personalities from reputed organizations, whowill enlighten the participants in the related fields. Please downloadthe brochure containing information and registration details alongwith this invitation for your kind perusal. We extend humbleinvitation to you and your colleagues to participate actively in theworkshop and make it a big success.It will be appreciated if you could inform to your colleague andstudents of your institute/organization. The National symposium cumworkshop on “RECENT TRENDS IN STRUCTURAL BIOINFORMATICS AND COMPUTERAIDED DRUG DESIGN” will be quite useful in various ways in differentfields such as Structural biology, System Biology, ComputationalChemistry and Pharmacogenomics.Call for Poster Presentations: All the participants are invited tosubmit an abstract of one page in English, describing their originalresearch related to the theme of this symposium cum workshop. Mailyour abstracts to bioinfoau@gmail.com.Please visit our website to get more details about the Workshop:www.bioinfoau.org/sbcadd'2012

2nd INTERNATIONAL CONFERENCE on BIOINFORMATICS AND SYSTEMS BIOLOGY

The genome – sequencing and structural genomics efforts worldwide have contributed to huge data on protein sequences and novel protein folds. However, there still remains a wide gap between the number of known protein sequences and three dimensional structures. The conference will deal to protein fold prediction, comparative protein modelling, secondary structure prediction, protein dynamics and simulations, ab-initio prediction and the validation of protein models and various aspects of structure determination and analysis by X – ray crystallography.

    Paper submission open December 2, 2010
    Paper submission deadline January 20, 2011
    Paper acceptance decision January 28, 2011
    Poster submission open December 30, 2010
    Poster submission deadline January 28, 2011
    Poster acceptance decision January 31, 2011
    Registration open December 2, 2010
    Early-bird registration upto January 31, 2011
    Conference Feb 16 - 17, 2011

Do you wish to know more?

Bioinformatics position

Courtesy Bioclues

Are you a skilled bioinformatician? Do you have experience with analysis and integration 

of large data sets? Would you like to work with leading experts and constantly improve 

your skills? Then you may be Intomics’ next bioinformatician.

We are expanding our bioinformatics team and are seeking a skilled bioinformatician to 

help the team provide innovative solutions for our clients in the pharmaceutical industry. 

You will play an important role in implementing data mining strategies for projects in 

areas such as target identification, biomarker identification, disease systems biology, and 

translation research.

Our preferred candidate has the following profile:

• Bioinformatics or computational biology background
• Experience with large-scale data mining
• Strong experience with programming (e.g.  Perl,  Python,  Java),  databases (e.g. MySQL, PostgreSQL), and Unix
• Excellent communication skills and the ability to work in a team
• Strong reporting and documentation skills
• A PhD in bioinformatics or systems biology is an advantage, but not a requirement
• A solid understanding of basic molecular biology
• Experience with several large scale data types is further an advantage

We are offering an  exciting and challenging job, where you get the opportunity to 

develop your skills and qualifications. You will get to work with interesting projects  in 

close collaboration with our clients.  Intomics A/S offers  a competitive salary  and  a 

friendly working environment. Some traveling must be expected.

Applications should be submitted electronically before 31st of January 2011 by email to 

applications@intomics.com marked with “application-1182” in the subject header.

Enquiries about the position can be made to CEO Thomas S. Jensen, tel: +45 88807979 

or  skot@intomics.com. All interested candidates irrespective of age, gender, race, or 

religion are encouraged to apply.

Extending pathways and processes using molecular interaction networks to analyse cancer genome data

This something really interesting to PPI, Systems biology  and molecular networks people, I just recently came across,

Cellular processes and pathways, whose deregulation may contribute to the development of cancers, are often represented as cascades of proteins transmitting a signal from the cell surface to the nucleus. However, recent functional genomic experiments have identified thousands of interactions for the signalling canonical proteins, challenging the traditional view of pathways as independent functional entities.

Combining information from pathway databases and interaction networks obtained from functional genomic experiments is therefore a promising strategy to obtain more robust pathway and process representations, facilitating the study of cancer-related pathways. 

Results: We present a methodology for extending pre-defined protein sets representing cellular pathways and processes by mapping them onto a protein-protein interaction network, and extending them to include densely interconnected interaction partners. The added proteins display distinctive network topological features and molecular function annotations, and can be proposed as putative new components, and/or as regulators of the communication between the different cellular processes.

Finally, these extended pathways and processes are used to analyse their enrichment in pancreatic mutated genes. Significant associations between mutated genes and certain processes are identified, enabling an analysis of the influence of previously non-annotated cancer mutated genes. 

Conclusions: The proposed method for extending cellular pathways helps to explain the functions of cancer mutated genes by exploiting the synergies of canonical knowledge and large-scale interaction data.

Author: Enrico GlaabAnais BaudotNatalio KrasnogorAlfonso Valencia

Credits/Source: BMC Bioinformatics 2010, 11:597

THOMSON REUTERS ACQUIRES GENEGO

Thomson Reuters today announced that it has acquired GeneGo, a leading provider of biology and disease information, analytics, and decision support solutions for pharmaceutical research and development.

Effective immediately, GeneGo will become part of the Healthcare & Science business of Thomson Reuters. Financial terms of the transaction were not disclosed.

The acquisition enables Thomson Reuters to provide the pharmaceutical, biotechnology, and academic research communities with solutions that provide better understanding of the underlying mechanism of disease and potential therapies. GeneGo’s scientific expertise and assets in biology-driven drug discovery complement the Thomson Reuters life sciences portfolio that covers drug pipeline competitive intelligence, patents, and chemistry.

do you wish to know more?

International PhD Program in the Biological Sciences

Under the auspices of the University of Tübingen, approximately 120 students from all over the world are working on their PhDs at the Max Planck Institute for Developmental Biology and the Friedrich Miescher Laboratory. Here, they profit from an interdisciplinary environment and first-rate scientific resources. Dedicated support and educational programs foster the scientific growth of doctoral students. The program offers cutting edge training in

• Bioinformatics
• Structural Biology
• Plant & Animal Development 
• Molecular & Cellular Biology/ Biochemistry
• Developmental & Quantitative Genetics
• Evolutionary Biology & Ecological Genetics
• The application deadline is November 24, 2010.

Do you wish to know more?

Positions open:PhD & Postdoc positions, Systems Biology, Finland

The Computational Systems Biology group led by Harri Lähdesmäki in the
Department of Information and Computer Science at Aalto University School of
Science and Technology (formerly Helsinki University of Technology) uses
computational and statistical modeling techniques to study molecular
regulatory mechanisms and biomolecular networks, and their role in health
and disease. We have interest in statistics, computational science and
molecular biology, and how modern computational methods can be applied to
experimental data to understand biological systems.

1.  Post-doc/Ph.D. studentship in computational systems biology
2.  Ph.D. studentship in computational systems biology
3.  Ph.D. studentship in statistical modeling and machine learning for next-generation sequencing data in systems biology
4.  Part-time research assistant (MSc student level) in bioinformatics/computational systems biology

Do you wish to know more?

4th Asian Young Researchers Conference on Computational and Omics Biology

The 4th Asian Young Researchers Conference on Computational and Omics Biology is jointly organized by the Joint-International Society for Computational Biology Student Council ISCB-SC Regional Student Group RSG Japan, Korea and Singapore; young researchers in Taiwan and the GCOE program “Genome BigBang” of The University of Tokyo, Japan.

The 4th AYRCOB aims to achieve a 2-fold objective:

1) To provide an avenue of exposure for students who are interested in the areas Computational and Omics Biology to participate in lectures of current topics from leading scientists of the field.

2) To establish international collaboration through interaction and discussion with fellow participants.

** Travel expenses of selected ORAL presenters will be FULLY COVERED by the conference sponsors! ** 

Key Dates

Wednessday, 25th August 2010: Call for Abstract Opens

Monday, 13th September 2010: Website Registration open

Monday, 25th October 2010: Abstract Submission Deadline

Friday, 5th November 2010: Abstract Acceptance Notification

Wednesday, 10th November 2010: Abstract Acceptance Deadline

1st to 3rd December 2010: Main conference (lectures, orals, posters, and discussions)

2rd to 3rd December 2010: 1st Joint Clinical Bioinformatics Symposium and Singapore Symposium on Computational Biology 2010

Do you want to know more?

India's First Symposium on Synthetic Biology

Centre for Systems and Synthetic Biology & Centre for Bioinformatics University of Kerala, Thiruvananthapuram, Kerala
Welcome to India's First Symposium on Synthetic Biology                       The event will address several strategic issues: 1. How to design organisms from scratch ? 2. Are we ready for the Computer Aided Design of organisms ? 3. Can we design stable genetic circuits for useful applications ? 4. Have we entered the era of ordering genomes by email ? 5. Is the emergence of biohacking, the next big thing in biology ? Invite you to this first synthetic biology meeting in India. The evolving synthetic biology community in our country needs to discuss unique ideas, interest groups, synergies, funding avenues and useful applications. The key goal will be to identify areas where India has potential to take global leadership.
		Welcome to BIODESIGN INDIA 1.0

Share |

'Omics Projects Snag More than $625M Worth of NIH Stimulus Grants

The National Institutes of Health has awarded 970 stimulus grants worth more than $625 million — around 14 percent of total NIH stimulus grant funding to date — to projects that fall within the broad family of 'omics disciplines, according to a preliminary analysis of the NIH funding database conducted by GenomeWeb Daily News.

As of Sept. 30, the close of the fiscal year, the National Institutes of Health had awarded a total of $5 billion in stimulus funding — nearly half of the $10 billion appropriation that NIH will disburse over two years under the American Recovery and Reinvestment Act of 2009.

The $5 billion figure includes both grants and contracts, however. For grants alone, NIH had awarded approximately $4.4 billion via 12,789 ARRA grants as of Oct. 7, according to the database.

The 970 grants awarded to 'omics projects comprise 7.5 percent of the stimulus grants awarded so far, but the total funding awarded to these projects makes up 14 percent of NIH ARRA grant funding to date.

The largest share of grants — 194 — went to bioinformatics and computational biology projects, for a total of $92.4 million in funding.

Sequencing projects snagged the most amount of total funding, however, with 88 grants worth $129.8 million.

Those disciplines were followed by:

• projects and centers focused on translational research and systems biology, which garnered 148 grants totaling $100 million;
• proteomics projects — including instrumentation grants for mass spectrometers and nuclear magnetic resonance systems — which were awarded 141 grants totaling $57.2 million;
• projects that involved RNAi, microRNAs, and other non-coding RNAs, which snagged 93 awards worth a total of $29 million;
• pharmacogenomics and personalized medicine projects, which were granted 80 awards worth $45.2 million;
• biochips and microarrays — excluding genome-wide association studies — which netted 63 awards worth $33.3 million;
• GWAS studies, which were awarded 28 grants worth $42.8 million;
• epigenomics projects, which received 38 awards totaling $26.1 million;
• metabolomics studies, which garnered 11 grants worth a total of $5.5 million; and
• metagenomics efforts, which received 8 grants worth $6.9 million.

There were 134 grants, worth a total of $113.6 million, awarded to genomics projects that did not fall into any of the above categories (see below for a breakout of the number of grants and the funding amounts awarded to each discipline).

The research institutes that picked up the lion's share of the 970 'omics awards were the University of Washington, with 27 grants worth $24.3 million; Harvard/Harvard Medical School with 26 grants worth $19.8 million; and the University of Michigan at Ann Arbor and Stanford University with 22 grants each worth $18.7 million and $11.8 million, respectively.

The University of Pennsylvania, Johns Hopkins University, and Brigham and Women's hospital were each awarded 19 'omics grants, worth $22.1 million, $10.7 million, and $12.5 million respectively.

The Broad Institute, which was awarded 14 'omics stimulus grants, snagged the most total funding, with $33 million.

The largest single 'omics stimulus award, worth $12.2 million, went to Eric Boerwinkle at the University of Texas Health Sciences Center for a project entitled, "Building on GWAS for NHLBI-Diseases: The CHARGE Consortium."

Other 'omics awards in the double-digit million range went to Wash U, which received $10 million for "Center for Large-Scale Genome Sequencing and Analysis;" the Broad Institute, which received $10.2 million for "Comprehensive Sequencing and Analysis of Variation in NHLBI Cohorts;" and the University of Washington, which received $11 million for "Northwest Genomics Center."

The average amount for 'omics stimulus awards was $644,807, compared to an average of $340,524 for all NIH ARRA awards.

---

Editor's note: the number of grants and total funding in the subcategories is greater than the 970 grants and $625 million cited in the article due to some grants being counted in more than one category.

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
  

Researcher at Molecular Connections develop a Alzheimer disease Pathways Compendium for inclusion at the Alzforum

This Pathways Compendium provides an index of Alzheimer disease pathway models contributed by researchers and companies.

Probable Interaction Networks Involved in Pathology of Alzheimer Disease: Predicting Targets and Therapeutic Agents - NetPro™ based Study. Developed by researchers at Molecular Connections Private Limited, an in silico discovery services company. Users can click on a specific node (molecule) to get information on all interactions of the molecule in the given network. Click on the interaction arrows for information on the specific interaction.

The Alzheimer Research Forum is a Pioneering Biomedical Web Community. Founded 13 years ago when the Web was still in its infancy, the "Alzforum" has more than 5,000 registered members and is familiar to most Alzheimer scientists in the world.


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
  

Systems Biology Can Uncover Signatures of Vaccination Immune Response

A team of American and French researchers used systems biology to identify gene signatures predicting human immune responses to the yellow fever vaccine, YF-17D. The work appeared in an advanced online publication in Nature Immunology yesterday.

Using high-throughput gene expression measurements, multiplex analysis of cytokines and chemokines, and multi-parameter flow cytometry, investigators tested samples taken from more than a dozen individuals in the days and weeks following their yellow fever vaccination. Computational modeling allowed them to come up with signatures predicting CD8+ T-cell and neutralizing antibody responses to YF-17D — insights into vaccine immunogenicity that may inform future vaccine research and development.

“The identification of gene signatures that correlate with, and are capable of predicting, the magnitudes of the antigen-specific CD8+ T-cell and neutralizing antibody responses provides the first methodological evidence that vaccine-induced immune responses can indeed be predicted,” senior author Bali Pulendran, an immunologist and virologist at the Emory Vaccine Center in Atlanta, and his colleagues wrote.

The yellow fever vaccine, which was developed in the 1930s, has been administered to more than 600 million people around the world. Because it is among the most effective vaccines to date — protecting 80 to 90 percent of the individuals who receive it — the researchers reasoned that YF-17D could serve as a good model for studying the early immune response to vaccination.

Do you want to know more?

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.

Position open Group Leader - Bioinformatics/Systems Biology

The Computational Biology Unit (CBU) has been established to conduct top-level European research in bioinformatics, and to serve functional genomics research in Norway with relevant training and services.

CBU is searching for an additional group leader. The group leader will carry out research in the field of computational biology/bioinformatics and contribute to the overall objectives of CBU. The group leader should have a PhD and post-doctoral experience including a solid publication record in a relevant subject. Candidates will be evaluated with emphasis on their ability to raise external funding and to supervise and carry out research projects. The research profile of the candidate should be within a relevant area for CBU. Candidates with profiles in direction of systems biology will be preferred. The group leader will direct a research group consisting of Ph.D. and post-doctoral scientists.

The CBU and its partners currently have bioinformatics research activities in the fields of protein biophysics, molecular modeling and protein dynamics, transcriptional regulation microarray and proteomics bioinformatics, and genome assembly and annotation. Activity has been initiated towards integrative bioinformatics and systems biology. There are excellent opportunities for collaboration with the molecular biological and biomedical as well as mathematical and informatics research groups in Bergen.

CBU is part of Bergen Center for Computational Science (BCCS) and located together with the Department for Informatics, the Molecular Biology Department and the SARS Centre for Marine Molecular Biology, a partner of EMBL. BCCS owns and operates large scale computing facilities that provide an excellent computational environment. CBU is partner in the Molecular and Computational Biology research school (http://www.mcb.uib.no). CBU is coordinating the bioinformatics technology platform for the national functional genomics programme (FUGE) in Norway.

Salary and professional resources are internationally competitive. Please send your CV, your ten most relevant publications, and a detailed statement of research interests to Professor Inge Jonassen (Inge.Jonassen@bccs.uib.no), head of the CBU. Evaluation of applications will commence January 4th 2009 and continue until a suitable candidate has been identified. For more information about CBU, please refer to http://www.cbu.uib.no/, or contact Inge Jonassen.

Courtesy:

Inge Jonassen, PhD

Department of Informatics and

Computational Biology Unit, BCCS

University of Bergen

HiB

No5020 Bergen

Norway

email: inge.jonassen@ii.uib.no

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.

Sequence Analysis is still sexy:Dual Descriptor Method for Biological Sequence Analysis

The emergence of “Systems Biology” in recent years highlights the systematic viewpoint of bio-system modeling. Building on such a background, Dual Descriptor Method, a generic methodology for biological sequence analysis is proposed. From a systematic perspective, Dual Descriptor is defined as a two element set of Composition Weight Map and Position Weight Function which aim at reflecting the composition and permutation information of a sequence. An alternate training algorithm is provided to get an optimum description of the building patterns of the sequences.

In this paper, dual descriptor method has been applied to the analysis of two typical problems of molecular biology: gene identification and the prediction of protein function. Satisfactory and insightful results are achieved. Owing to the generality of this methodology, dual descriptor method has wide application perspective for many problems of pattern recognition, especially those involved in “Systems Biology”.

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.

Enter Little b, a computational language that can penetrate the "mind" of a cell.

DNA is pretty straight forward. With its simple composition and linear structure, it easily lends itself to mathematical models. Not so with proteins. In fact, proteins are an order of magnitude more complex than DNA. It is proteins, not DNA, that carry out the cell's heavy lifting. However, with their intricately folded three-dimensional shapes determining a seemingly endless range of possible functions and their manifold interactions with other proteins and with DNA, the leg-work required to mathematically capture the protein universe seems absurd.

That is why a team of Harvard Medical School researchers have decided to attack this issue from an entirely new angle. Rather than build a mountain range of proteomic data one grain of dirt at a time, they have developed a computer program that can take on the responsibility of assembling such a gargantuan model.

"Through incorporating principles of engineering, we've developed a language that can describe biology in the same way a biologist would," says Jeremy Gunawardena, director of the Virtual Cell Program in Harvard Medical School's department of systems biology. "The potential here is enormous. This opens the door to actually performing discovery science, to look at things like drug interactions, right on the computer."

These findings will be published in the July 23 issue of Journal of the Royal Society Interface.

"Programming with models: modularity and abstraction provide powerful capabilities for systems biology"

Aneil Mallavarapu, Matthew Thomson, Benjamin Ullian, and Jeremy Gunawardena

Department of Systems Biology, Harvard Medical School, Boston MA

Mallavarapu used the programming language LISP, a language widely used in artificial intelligence research. LISP is famous among computer scientists due to its ability to write code that, in turn, can write code, enabling a programmer to derive new mini-languages.

"LISP isn't like typical programs, it's more like a conversation," says Gunawardena. "When we input data into Little b, Little b responds to it and reasons over the data."

For example, Gunawardena's lab works on kinases, a kind of protein that transfers phosphate chemicals to other proteins in order to regulate their activity. While this property is common to all kinases, there is a great deal of variety in how particular kinases carry this out. Little b, however, understands this basic property of kinases, this abstraction.

Here, the researchers demonstrated how they were able to interact with Little b to build complex models of kinase activity, using Little b as a kind of scientific collaborator, and not simply a passive tool.

"This language is stepping into an unknown universe, when your computer starts building things for you," says Gunawardena. "Your whole relationship with the computer becomes a different one. You've ceded some control to the machine. The machine is drawing inferences on your behalf and constructing things for you."

"The next step is to create an interface that's easy to use," says Gunarwardena. "Think of web page development. Lots of people are creating web pages with little or no knowledge of HTML. They use simple interfaces like Dreamweaver. Once we've developed the equivalent, scientists will be able to use our system without having to learn Little b."

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.

VisANT: an integrative framework for networks in systems biology

Integrative Visual Analysis Tool for Biological Networks and Pathways

Already blogging on the topic Structured Digital Abstracts - Easier Literature Searching dicussing the inportance of networks in the form of interactions, and further in several others about visualization tools, here is one more.

The essence of a living cell is adaptation to a changing environment, and a central goal of modern cell biology is to understand adaptive change under normal and pathological conditions. Because the number of components is large, and processes and conditions are many, visual tools are useful in providing an overview of relations that would otherwise be far more difficult to assimilate. Historically, representations were static pictures, with genes and proteins represented as nodes, and known or inferred correlations between them (links) represented by various kinds of lines. The modern challenge is to capture functional hierarchies and adaptation to environmental change, and to discover pathways and processes embedded in known data, but not currently recognizable. Among the tools being developed to meet this challenge is VisANT (freely available at http://visant.bu.edu) which integrates, mines and displays hierarchical information. Challenges to integrating modeling (discrete or continuous) and simulation capabilities into such visual mining software are briefly discussed.

Do you want to more?

The Beta Workbench: a computational tool to study the dynamics of biological systems

The Beta Workbench (BWB), a scalable tool built on top of the newly defined BlenX language to model, simulate and analyse biological systems. Show the features and the incremental modelling process supported by the BWB on a running example based on the mitogen-activated kinase pathway. Provide a comparison with related approaches and some hints for future extensions.

Do you want to know more?