Application Support Specialist Job at Monsanto

Monsanto is a Fortune 500 Company, headquartered in St. Louis, Missouri. It has more than 20,000 employees at 320 locations worldwide in four primary regions – Europe/Africa, Asia Pacific, Latin America and North America. It has $11.7 billion in annual sales. In India, it started his operation in 1949 and is headquartered in Mumbai.

Post : Application Support Specialist – Contract
No of Post : Two
Experience : 3 to 7 years
Location : Bangalore
Job Description : The successful candidate will become a member of Technology Pipeline Solutions (TPS) Team, part of Monsanto IT systems, supporting enterprise-level biotech and breeding related software applications. This is a very domain intensive role and will require deep understanding of various concepts in breeding, Biotechnology and data base applications.
Job responsibilities :
1. Quick grasping of enterprise applications and their usage
2. Train the scientific community and ensure effective utilization of applications
3. Day to day interaction with scientists and breeders to provide quality & timely support
4. Proactive in identifying the customer needs, arriving at probable solutions, working closely with IT teams for better solutions
5. The individual will need to interact closely across global teams
Educational Qualification : B.Sc – Agriculture, Bio-Chemistry, Biology, Botany AND M.Sc – Agriculture, Bio-Chemistry, Biology, Botany
Desirable :
a. More then 3 years of Breeding/Plant/Biotech Research experience
b. Work experience with scientific data base/ Bioinformatics applications is desirable.
c. Strong oral and written communication skills, collaboration and networking skills across scientific and international teams, self motivated, strong team player

Contact Details :Executive Name : Rahul Anand
Email Address : rahul.anand@monsanto.com

Deadline : 02.03.12

PerkinElmer Signs Agreement to Acquire CambridgeSoft Corporation

PerkinElmer, Inc., a global leader focused on the health and safety of people and the environment, today announced that it has signed a definitive agreement to acquire CambridgeSoft Corporation, and has completed the purchase of ArtusLabs, Inc. 

These acquisitions will enhance the Company's focus on knowledge management in laboratory settings by expanding its informatics and software offerings, enabling customers to rapidly access and share enterprise-wide data for faster, more informed scientific decisions.

The purchase of CambridgeSoft is expected to close in the second quarter, subject to customary closing conditions, including the expiration or termination of the waiting period under the Hart-Scott-Rodino Antitrust Improvements Act.

Do you wish to know more?

Python Text Processing with NTLK 2.0 Cookbook - Ebook Free Download

Python Text Processing with NTLK 2.0 Cookbook - Ebook Free Download

OPENING - Manager or a Senior Bioinformatician

A manager or a senior bioinformatician is required.

Qualifications:- A Master degree in biology, bioinformatics
(or a related discipline), or equivalent experience in bioinformatics
in the pharmaceutical or biotech industry. 
An MS or Ph.D. is strongly preferred.

Required Skills:-Strong technical, analytical, and problem 
solving skills, Strong communication abilities, A dedication
to software development best practices and methodologies

Experience: - 2+ years experience developing software solutions
in the pharmaceutical R&D or biotech sector, Demonstrated
ability with several of the following: Java, Java/J2EE, 
.NET (VB, C#, ASP), Sharepoint, Oracle, JDBC, SQL, 
Unix/Linux, Windows, Mastery of at least one programming
language/platform.

Company:- MNC Bioinformatics.

Location:- Bangalore, Hyderabad and Pune.

Salary:- 15-20 lacks.

Further relevant information can be accessed from the given website:-

http://www.bixee.com/manager-bioinformatics-sr--jobs-at-mnc-bioinformatics-7243.html/

Bioinformatics Workshops @ Lucknow

Workshop: Developing Bioinformatics applications with Bioperl 
Duration: 5 days, Registration Fee: Rs. 2000 /-  
Starting date: November 05 - 09, 2010 

Workshop: Biological sequence analysis
Duration: 3 days, Registration Fee: Rs. 1000 /-
Starting date: November 26 - 28, 2010 

Venue:The Bioinformatica Solutions,lucknow

Fee should be deposited through bank draft in the name of

"The Bioinformatica Solutions" payable at Lucknow. 

Follow this link to apply http://www.thebioinformatica.com/Registration.htm 

Application of Next Generation Sequencing Technologies as Shared Research Resources

Lectures presented by Dr George Grills, Director of Operations of Core Facilities in the Life Sciences, Cornell University. 


http://www.mgrc.com.my/ess_Dr_George.shtml

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A comparison of common programming languages used in bioinformatics

The electronic version of this article is the complete one and can be found online at:http://www.biomedcentral.com/1471-2105/9/82

Abstract

Background

The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python.

Results

Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found.

Source code and additional information are available from http://www.bioinformatics.org/benchmark/webcite

Conclusion

This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language.

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CLC Bio along with partners received a $2 million grant from the Danish National Advanced Technology Foundation

CLC Bio today said that it, along with partners Ion Torrent Systems and Aarhus University Hospital, have received a $2 million grant from the Danish National Advanced Technology Foundation to support a molecular diagnostics collaboration.

Under the three-year alliance, the partners aim to develop and integrated hardware and software solution for molecular diagnostics that will utilize high-throughput sequencing. According to CLC Bio, the partners aim to provide faster and more precise DNA-based diagnostics.

Earlier this year, Ion Torrent unveiled its Personal Genome Machine, an electronic sequencer last week that reads DNA on a semiconductor chip by measuring the release of hydrogen ions as nucleotides get incorporated by DNA polymerase. The PGM sequencer is a desktop instrument that will cost only $50,000.

The Ion PGM sequencer does a single run in about an hour or two. The collaboration will lead to an IT solution that can be used for molecular diagnostics research and for clinical diagnostics applications.

Science jobs from Polyclone Bioservices Pvt. Ltd.

Science jobs from Polyclone Bioservices Pvt. Ltd.

Location:Bangalore(India)

Designation: Scientist (Bioinformatics)
Qualifications: M.Sc/ PhD
Experience: 0 – 1 yrs

Requirements:

• Candidates will have strong knowledge using–and coding functionality that
interacts with–public nucleotide and protein sequence databases, sequence
alignment software, and related computational genomic resources.

• Strong background in sequence analysis, genome annotation, analysis of
gene or protein expression, protein structure or docking prediction,
comparative genomics is a must. A broad knowledge of statistics and
statistical methods used in analyzing genomics data is preferred.

Desirable:

• C# under the .Net Framework as well as Perl.
• Knowledge of the R\Bioconductor programming language
• Strong background in multi-univariate and Bayesian statistics, and some
experience in machine-learning techniques (SVM, NN).
• We welcome expertise in Python, Bioperl, Ruby, Java, C++/C, and Matlab
• Understanding of scientific workflows, laboratory instrument interactions
and scientific data
• Ability to discuss informatics software specifically, bioinformatics,
chemo informatics,LIMS, SDMS, other Life Science analytical applications, at
varying levels of detail
• Ability to gather market / prospect requirements and scientific use cases
and contribute to effective implementation of scientific use cases in
complex data environments
• Writing research papers, posters, participation in conferences seminars

Website:http://www.polyclonebio.com

Note: Application expires on 28th April,2010

Several positions open at Polyclone, Biobase, ocimumbio...

Several position

http://www3.ocimumbio.com/about/careers/

http://www.mgrc.com.my/careers.shtml

http://www.biobase-international.com/index.php?id=400

http://www.polyclonebio.com/opportunities.html

http://www.genedata.com/company/careers/ch-gdp-2006.html

http://www.biomatters.com/default,24,careers.sm

http://www.atgclabs.com/Jobs.html

http://www.clcbio.com/index.php?id=12

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CambridgeSoft's Business Partner in Kochi, India is hiring

CambridgeSoft's Business Partner in Kochi, India is hiring for multiple positions.

The following is a list of available positions:

• Lead Developer - Desktop - ChemBio3D (Kochi, India)



• Developer - Enterprise - Network Communication and Distributed Computing (Kochi, India)



• Developer - Desktop - User Interface (Kochi, India)



• Developer - Desktop - Numerical Methods (Kochi, India)



• Lead Developer - Enterprise - Inventory (Kochi, India)



• Lead Developer - Enterprise (Kochi, India)



• Developer - Enterprise - (C++) (Kochi India)



• Developer - Enterprise - E-Notebook Support Analyst (Kochi, India)



• Developer - Desktop - ChemDraw (Kochi, India)



• Lead Developer - Enterprise - E-Notebook (Kochi, India)



• Developer - Enterprise - Database Specialist (Kochi India)



• Developer - Desktop – Core Chemistry Team (Kochi India)



• Developer - Desktop - Chemical Database (Kochi, India)

All positions in Kochi, India are full time with our business partner. Details can be found online at:
http://www.cambridgesoft.com/careers/?category=&country=89

Position Type: Full Time
Location: Kochi, India

To submit resumes via email, please email careers@cambridgesoft.com. Please be sure to include the Job Code in the subject line.

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
  
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Bangalore unveils new BT policy

In effort to make Karnataka Biotechnology Capital of Asia, the State government, on Wednesday, launched ‘Millennium Biotech policy II’ a successor to Biotech Policy issued of 2001.

Releasing the policy, Principal Secretary IT, BT S&T Ashok Kumar Manoli said the new policy will provide all fiscal incentives and concessions under Karnataka Industry policy 2009-14 to bio technology industry and the R&D centres. Biotech organisations will get incentives including a subsidy of 50 per cent for setting up effluent treatment plants. The financial incentives includes assistance for patent tracking and patent registration. According to the new policy biotech will be treated as special industrial consumers and provided with dedicated power lines that are exempt from power cuts. It also assures power connection to biotech companies within 10 days of applications. Bioinforamtics companies that use up to 50 KVA power will be permitted to be established without any local restrictions. The Biotech unit will be exempted from electricity duty of 100 per cent. The government also express its commitment and importance of creating a start up ecosystem and the government will encourage setting up of venture capital funds for biotech industries called KBIO-Ven fund of Rs 50 crore. Companies with focused area on transgenics, stem cell biology, bio manufacturing and other social relevance will be eligible for funding. A separate fund of Rs 15-20 crore will be used to issue grants in the range of Rs 10-20 lakh for firms that translate research to commercial projects. The government will also offer tillable agricultural land of 15-20 acres of land and solely for agriculture related bio tech field trials and experiments for a period of 35 years. All R&D labs will be automatically come under the green category, and omitted from pollution control board permission for setting up labs. The government will set up ten BT finishing school selected by vision group. The government will provide financial support to the schools to set up lab instruments and other technology related gadgets to train students. It will also provide specific infrastructure for the development of biotechnology. This includes promoting of Hi-tech bio tech park in the state. A 106 acre Biotech park Bangalore Helix is coming up in Electronic City. A Bio-IT park in a 100 acre plant in Ramanagaram is also planned.

Click here for the Policy. Note: File size - 18 mb

Launch of Millenium BT Policy

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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
  

CambridgeSoft's Business Partner in Kochi, India is hiring for multiple positions

CambridgeSoft's Business Partner in Kochi, India is hiring for multiple positions. If you know any appropriate candidates, with a chemistry or biochemistry background.

The following is a list of available positions:

• Team Lead - coordinating the activities of small software development teams: http://www.cambridgesoft.com/careers/details/?Career=115
• 3D Team Leader: http://www.cambridgesoft.com/careers/details/?Career=228
• Developer - Network Communications and Distributed Computing: http://www.cambridgesoft.com/careers/details/?Career=230
• Developer Numerical Methods: http://www.cambridgesoft.com/careers/details/?Career=234
• Senior Lead Developer: http://www.cambridgesoft.com/careers/details/?Career=225
• Scientific Software Developer C++: http://www.cambridgesoft.com/careers/details/?Career=14
• Lead Developer E-Notebook: http://www.cambridgesoft.com/careers/details/?Career=81
• E-Notebook Enterprise Support Analyst: http://www.cambridgesoft.com/careers/details/?Career=27
• ChemDraw Developer: http://www.cambridgesoft.com/careers/details/?Career=70

All positions in Kochi, India are full time with our business partner. Details can be found online at: http://www.cambridgesoft.com/careers/?category=&country=89

Position Type: Full Time
Location: Kochi, India

To submit resumes via email, please email careers@cambridgesoft.com. Please be sure to include the Job Code in the subject line.

The Indian Bioinformatics Landscape

Pharmaceutical companies are under constant pressure to develop new "blockbuster" drugs to replace older ones that are going off patent. With costs to launch a new drug crossing $1 billion and the number of drugs approved for commercial launch decreasing, pharmaceutical companies are increasingly looking at biotechnology to deliver results.



Traditional "big pharma" companies currently account for about 65% of total R&D expenditure but they have a share of less than one third of drugs in the pipeline. On the other hand, smaller biotech companies account for 35% of total R&D spending with almost two thirds of the total drugs in pipeline. With bioinformatics increasingly becoming the backbone of drug research, the bioinformatics market is piggybacking on the investments made in drug discovery and development, and finds application in every stage of the pharmaceutical and biotech R&D process.

The global bioinformatics market of about $2.3 billion is expected to grow at a CAGR of 16% over 2007-2010 to reach $3.6 billion by 2010.

The rapid rise of the genomics industry and its increasing application in biotech and pharmaceutical R&D have created a huge commercial market for bioinformatics due to the large amount of data being generated. We believe that almost all new drug discovery programs will be based on genomics in future and, the pressure to reduce cost and time of new drug development will lead to increased outsourcing of bioinformatics services.

Indian Bioinformatics Opportunity

Outsourcing to India, compared to other developed countries, offers about 30-40% costs savings in overall drug discovery research, and close to 60% cost savings when outsourcing core bioinformatics services. This is due to the lower wage costs for skilled manpower, and lower infrastructure costs.

The Indian bioinformatics market has grown from $18 million in 2003-04 to $35 million in 2006-07, at a CAGR of 25%. Interestingly, owing to low local demand, $32 million or about 90% of bioinformatics revenues in India are derived from outsourcing activities. "Local demand for bioinformatics services is low due to low investment in new drug discovery. Even though research investments of life sciences companies are increasing, they are still small compared to global standards" says Ashutosh Mundkur, VBU Life Sciences, Service Offerings, Satyam Computer Services Ltd.

The Indian bioinformatics outsourcing services opportunity is estimated to grow at 25% per annum during 2007-2010 raising its share of the global market from 1.4% in 2007 to 1.7% in 2010. These estimates are made based on the current plans of Indian vendors, as well as considering the impact of scarcity in human resources. Improved availability of skilled workers could help take growth rates higher. Similarly, positive actions by the Indian government to enhance IP rights could also help raise growth.



Industry Structure

The Indian bioinformatics industry comprises vendors with origins in the life sciences domain or the IT domain. We estimate that there are about 45-50 companies active in the bioinformatics segment in India. Of these, about 35 are involved in the development of software tools, database solutions and providing bioinformatics services; the remaining largely into marketing third party products and services.

Vendors can also be segmented as domestic pure play bioinformatics companies, domestic IT companies, domestic life sciences companies, multinational IT and multinational pure play bioinformatics companies in India.



Vendor Capabilities

Pure play and life sciences companies have strengths in discovery informatics with niche offerings in data mining and visualization, and databases, while IT companies have a wider portfolio that includes clinical trial informatics as well as capabilities in data mining, visualization, integration tools, and databases.



Pure play companies, Ocimum Biosolutions and Strand Life Sciences have the highest level of specialization and focus on bioinformatics. Indian and multinational IT companies such as IBM, Mphasis, TCS, HCL Technologies, and Infosys are less focused on the life sciences vertical. Avesthagen and Jubilant Biosys are CRAMS companies also offering bioinformatics services. Their level of specialization and focus is higher than (domestic and multinational) IT companies but their core business is contract research and/or manufacturing.



Key Trends

Focus on target validation techniques - Advances in genomics and sequencing has made target identification easier through bioinformatics tools. The focus of bioinformatics in the drug discovery process has therefore shifted from target identification to target validation.

Laboratory Information Management System (LIMS) tools - LIMS are tools that help automate collection and management of data generated in a laboratory. The market for LIMS products in India is estimated at $23 million in 2007, and is expected to grow at above 30% over 2007-2010.

Trend towards enterprise solutions - Presently, majority of the bioinformatics revenues are derived separately from databases, services and software products. Hardly any vendor provides a complete enterprise solution. Driven by the need for integration of various databases/tools with R&D efforts, in the future, enterprise IT solutions should garner a larger share of the market.

Long-term single vendor contracts - Companies with presence across various geographies require bioinformatics services on a global scale and often seek a single vendor that can offer a comprehensive range of services on a long-term basis, across the world. Understand and integrate a wide spectrum of emerging technologies with existing systems.

Forward and backward integration - Pure play companies are opting for forward integration into contract research services, while pharma/Contract Research and Manufacturing Services (CRAMS) companies are also providing (or looking to provide) bioinformatics services.

Inorganic growth - Several vendors are opting for strategic partnerships to strengthen their ability to scale, add to their service portfolio or increase client reach.

Outsourcing of discovery informatics - Global companies were earlier outsourcing only clinical research related services to India. The implementation of Intellectual Property Rights (IPR) in India from January 2005 is gradually bringing global companies to India also for discovery services involving sensitive data.

Challenges and Critical Success Factors

Indian bioinformatics vendors have a huge opportunity in bioinformatics services, customization of existing products and database licensing/creation/manipulation. However, they face certain challenges:

Standardization of Service Platforms & Modular Systems
Bioinformatics vendors work with varying standards and platforms. A major challenge is standardization of service platforms. Also, there is a need to offer more modular systems that can plug into other systems or well-documented application program interfaces already being used by their clients.

Problem of Market / Data Heterogeneity (Flexible tools)

Life Sciences companies may use different data formats, leading to incompatibility. Hence, it is a challenge for vendors to develop data integration tools to facilitate analysis of data sets from different sources. "Flexibility of a bioinformatics tool is essential for it to be a success. The tool should be flexible and allow for use in various applications," says Ajoy Singh, senior coordinator sales, Technoconcept (India) Pvt Ltd.

Tools must be adaptable, readily configurable to support access to new data sources, instruments, tools and new functionality requirements.

Domain Knowledge and Experience

Bioinformatics is a highly specialized field where domain knowledge is more important than just cost. Lack of biological understanding can result in sophisticated computational methods being applied naively thereby leading to under-utilization of advanced tools. Hence finding the right team is vital.

Niche focus

Industry experts believe that vendors must focus on select niche areas. Positioning generic software skills with a wide range of varied services could result in a very non-specialized service portfolio. Pure play vendors in contrast have inherent niche offerings, such as LabVantage's in LIMS, and Ocimum Biosolutions in microarrays.

"Technologies like SaaS offer a unique opportunity for an Indian player to break into the stronghold of globally established players such as Accelrys. Indian bioinformatics companies can re-architect their drug discovery offerings to the SaaS platform to scale up penetration into smaller biotech companies, which wouldn't necessarily want to go for expensive products." says Apurva Chamaria, group manager, Life Sciences, Healthcare, Retail, CPG & 3 PL, HCL Technologies Ltd.

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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.

Market study reveals 20 per cent growth for ELNs

Atrium Research has published the 2008 Electronic Laboratory Notebook Survey. This study contains the results and analysis of a survey of information technology, management, and scientific personnel in the life sciences, chemical, academic, government and food markets. Comprehensive data and analysis are reported on dozens of questions answered by 527 professionals from more than 20 countries. The report highlights user and prospective user opinions on data management challenges, technology interest, motivations, project goals, purchase timing, integration needs, and supplier product and brand perception.

According to the report, the market for ELNs is exploding, with more than 30 suppliers offering commercial solutions. One of the fastest growing informatics markets with a growth rate of nearly 20 per cent per year, ELNs are radically improving the effectiveness of laboratory operations. ELNs enable new approaches to knowledge management, collaboration, and data integration.

'We project sustained double-digit growth for ELNs for at least the next three years,' said Michael H Elliott, founder and CEO of Atrium Research. 'Our study shows the use of the technology expanding beyond early adopters in research synthetic chemistry into domains such as biology and analytical chemistry. Commercial life sciences continue to lead adoption; more than 30 per cent of biopharmaceutical companies have installed an ELN in at least one department.'

2008 Electronic Laboratory Notebook Survey

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.

Harnessing the power of multicore using PERL

How many of us really use our multi-core processors to the fullest extent? here is a blog article which gives some cool tips using PERL to exploit the power of your multi-core. I found this very interesting, Check it out


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.

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IBM to provide a server platform for analyzing protein structure and function.

Bioinformatics firm Biosof said today that it is working with IBM to provide a server platform for its PredictProtein product for analyzing protein structure and function. The collaboration will enable Biosof’s customers to use ProteinPredict through a virtual private network or on-site installation while running IBM’s high-performance computing hardware, New York-based Biosof said in a statement.

“Working with IBM provides our customers the unique opportunity to combine a secure infrastructure and cutting-edge hardware needed to run our highly resource-intensive algorithms,” said Burkhardt Rost, a manager of Biosof.


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.