Bio Saga Blog - A Chronicle of Life Sciences & Informatics

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This is no Sci-Fi but reel to real! Yes we can in deed program the DNA for real Now!  Bioinformatics scientists have built two logic gates for what they hope will become a new programming language for drug design as well as chemical and agricultural product engineering. The accomplishment seems hardly noteworthy except that these logic gates are made of E. coli. The two computational switches are based on two strains of the common bacterium. Researchers are now working to assemble them to perform computations. This genetic programming software would resemble any other programming language, says Kevin Clancy, senior staff scientist for bioinformatics at Life Technologies Corp. The Carlsbad, CA, company is funding the work, which is being done by researchers at the UC San Francisco School of Pharmacy. Life Tech plans to commercialize the technology. The software would convert instructions into a DNA sequence to be inserted into a bacterial, yeast or mammal cell. "It allows you ...

Courtesy: B ioclues Job Reference: G586-10LL Genome Discovery Unit, The John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment We are seeking a Genome Computational Specialist to support the work of researchers engaged in cutting-edge projects involving analysis of high throughput sequencing data. Location Canberra/ACT Term of Contract Permanent Grade ANU Senior Manager 1 (Information Technology) Salary Package $88,417 - $92,781 pa plus 17% superannuation Closing Date 3 January 2011 Position Overview The ANU's genomic strategies and expertise has positioned it as a key partner in a number of national and international genomics / phenomics research consortia. The ANU is underpinning this excellence in genomic biology by establishing a Genome Discovery Unit (GDU) for the analysis of high throughput sequencing data. The facility will be staffed by highly skilled personnel who will provide the core expertise for constructing and operating a h...

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 t...

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  

Organization:  Harvard Medical School Job Location:  Harvard Medical School, Boston, Massachusetts, USA Salary:  $50,000/year Benefits:  Family health insurance, T-Pass discount, credit union, child-care scholarships Job Description:  Post-doctoral position.Available immediately. Permanent residency not required. Working at the interface of biology, statistics, and computing, the candidate will analyze high through-put gene expression microarray data in cancer genomics. The goal is to develop novel data analysis algorithms and software and to identify genomic signatures in cancer patients and tumor-bearing mice. Requirements:  Qualifications: (i) PhD in bioinformatics, biostatistics, computer science or related fields; (ii)familiarity with molecular biology and genomics; (iii)strong programming skills (R, C++, Python): and (iv) proficiency in microarray software Bioconductor, dChip, and GenePattern. Contact Information:  Please send CV, a caree...

CambridgeSoft's Business Partner in Hyderabad, India is hiring for multiple positions. Appropriate candidates, with a chemistry or biochemistry background, could apply. The following is a list of available positions: Lead Developer - ChemDraw product on a Java platform (Hyderabad, India) Developer - JAVA DEVELOPERS (Hyderabad, India) Lead Developer - Desktop - ChemBio3D (Hyderabad, India) Developer - Enterprise - Network Communication and Distributed Computing (Hyderabad, India) Developer - Desktop - User Interface (Hyderabad, India) Developer - Desktop - Numerical Methods (Hyderabad, India) Lead Developer - Enterprise - Inventory (Hyderabad, India) Lead Developer - Enterprise (Hyderabad, India) Developer - Enterprise - (C++) (Hyderabad India) Developer - Enterprise - E-Notebook Support Analyst (Hyderabad, India) Developer - Desktop - ChemDraw (Hyderabad, India) Lead Developer - Enterprise - E-Notebook (Hyderabad, India) Developer - Enterprise - Database Specialist (...

Job Title:  Java Developer - Bioinformatics Salary:  35000-45000 Per Annum Excellent benefits Location:  Surrey Description:  Java Developer, Permanent, Guildford, £35-45k + excellent benefits and package Is a leading software solutions company for the pharmaceutical industry. A new opportunity has become available for a Java Developer with Bioinformatics to join a dedicated team to help develop software solutions to accelerate the drug discovery process. Key responsibilities include: Designing and implementing new products; maintenance work on existing products; mentoring other developers; helping to evangelize technology and component use throughout the company. The successful candidate will be a Java developer with a strong understanding of Bioinformatics. The ideal candidate will also have a working knowledge of J2EE/ JBOSS, Java Swing, JavaScript libraries and SQL but this is a nice to have. Please contact Tom Hildreth for immediate consideration and...

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 d...

Pfizer UK-Kent-Sandwich Computational Biologist Computational Sciences are integral to Pfizer’s strategy to accelerate the discovery of important new medicines. This is your opportunity to join a dynamic, innovative team, focusing on the development and use of novel computational methods and algorithms to enhance the efficiency and effectiveness of drug discovery. We are looking for a Computational Biologist with skills in working with genomics data, developing novel algorithms and generating new biological hypotheses to join our Computational Sciences Center of Emphasis in Sandwich, UK. Specific areas of interest include: • Identification of new datasets and data mining techniques relevant to drug discovery • Developing and testing novel methods and algorithms, working with academic collaborators where opportunities arise • Building and testing prototype systems (both interfaces and algorithm libraries) • Working with scientists to apply tools to every day problems • Awarded or...

Senior Bioinformatics Analyst Requirements: - PhD or equivalent experience in life science / biology. - 4+ years demonstrated success in working in the life sciences, preferably in an industry research settings. -In-depth understanding, analysis and processing of data from various post genomic technologies and their applications. - In-depth knowledge in gene expression (genotyping, chromosomal copy number, SNPs, gene signatures) and sequencing -Wide understanding of commercially available bioinformatics/clinical genomics tools and databases -Ability to handle complex / multi projects in rapidly changing environment. - Good knowledge on Perl, C / java and any relational databases. Responsibilities: - Analyzing and documenting project requirements. -Developing biocomputing algorithms for tools development and data analysis. -Performing biological analysis on data from various domains like gene expression, sequencing , molecular lab. -Co-ordination with sales team on projects to understan...

BioSLAX is a new live CD/DVD suite of bioinformatics tools that has been released by the resource team of the BioInformatics Center (BIC), National University of Singapore (NUS). Bootable from any PC, this CD/DVD runs the compressed SLACKWARE flavour of the LINUX operating system also known as SLAX . SLAX is becoming the live CD/DVD of choice because of its ability to modularize almost any application and plug it into the system on the fly. The system can also be installed to USB thumb drives or directly to the PC as a regular Linux using the BioSLAX installer provided. It consists of commonly used Bioinformatics Applications, Software and Algorithms. For Download, http://www.bioslax.com/downloads.shtml

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 o...

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 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

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: h...

The Oxford University Image Bioinformatics Research Group wishes to appoint a Computing Officer – Web Applications and Data Management to work on the JISC-funded ADMIRAL Project - A Data Management Infrastructure for Research Across the Life Sciences . This will involve interactive working with researchers to improve the management, archiving and Web Publication of their biological research data, undertaking Web application development, and system evaluation and maintenance of the data management infrastructure. Applicants should have a good B.Sc. or higher degree, probably in maths or science, and show evidence of creativity and research competence. Good programming and data management skills are required, as is familiarity with the standards and principles of modern Web application development. Experience with agile development techniques, Javascript, JQuery, Java, Python and RDF, and competence in Linux computer systems administration would be desirable. Further details about this...

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/de...

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 Be...

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 accur...

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 ...