The 4th Virtual Training Workshop on Bioinformatics

The 4th Virtual Training Workshop on Bioinformatics will be held on September-October, 2010, which is organized by Asian Bioinformatics Research and Education Network (ABREN). You are welcome to join the workshop. It covers more useful lectures on bioinformatics. The registration procedure is simple. Just you click the link which attached bellow. They will enable the accounts and send you e-mail with the account information, just before the workshop starts. 

Workshop and registration site: http://www.abren.net/workshop/

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Java Developer - Bioinformatics

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 full company details. No terminology in this advert is intended to discriminate on the grounds of age, and we confirm that we will gladly accept applications from persons of any age for this role. TRG provides services as an agency and an employment business.


Click here to view and apply for this job online 


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Two interesting bids on the billboard Genzyme and Ascendis Pharma

Courtesy Bloomberg

Sanofi-Aventis may begin a hostile bid for Genzyme Corp. should the U.S. biotechnology company resist a takeover approach, analysts at Citigroup Inc. said.

No other bidder is likely to emerge for Cambridge, Massachusetts-based Genzyme, and Sanofi will probably succeed in acquiring the company for $74 to $77 a share, Citigroup analysts Mark Dainty and Yaron Werber wrote in a report to clients today. Genzyme is worth $70 a share based on estimated cash flow, and Sanofi would benefit from as much as $5.50 a share of synergies in an acquisition, they said.

Investors in Genzyme say Paris-based Sanofi may have to pay at least $80 a share, or $21.3 billion, to acquire the maker of drugs that fight genetic diseases. Sanofi Chief Executive Officer Chris Viehbacher has support from his board to offer as much as $70 a share, or about $18.7 billion, and is preparing a formal offer letter, three people familiar with the situation said last week.

Novo Nordisk A/S, Novartis AG’S Sandoz and Eli Lilly & Co. are among bidders for Ascendis Pharma A/S of Denmark,  

The Copenhagen-based health-care company received offers of about $400 million, said the person, who declined to be identified because the process isn’t public. Ascendis may choose a final bidder by early September.

Ascendis has a technology that allows drugs to be released into the body in a controlled way over time, according to its website. The company focuses on hormone-related disorders and is developing a human growth hormone that can be taken once a week. It’s also developing new formulations of approved medicines and products for central nervous system and infectious diseases, according to the website.

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Microarray Data Analysis using R and Bioconductor

 IMPORTANT DATES for Course 
 Deadline for applications: August 30th 2010 
 Notification of acceptance dates: 
        EARLY: August 15th 2010 (only on special request, see Application) 
        NORMAL:August 30th 2010 
 Course date: September 6th to September 10th 2010

Course description: This course aims to introduce researchers to a multidisciplinary approach to microrray data analysis. Particular attention is devoted to the design of microarray experiments, data normalization and quality control as well as to statistical analysis. Participants might find the provided basic training invaluable for: how to approach designing microarray experiments planned in their lab; gaining knowledge and understanding of microarray analysis and quality issues; gaining confidence in performing preprocessing, quality assessment, and differential expression and downstream analysis using the statistical software environment R and some R libraries in Bioconductor, namely limma. The course also covers more specific topics, such as the analysis of Illumina and Affymetrix, as well as SNP and CNV data. Target audience: All aspects of the course are aimed at non-statisticians, suitable for beginners in microarrays as well as those who have already been working in genomics. The course may also be useful to computational biologists new to microarray analysis. The course is intensive so a highly motivated group of trainees, looking forward to dealing with microarray data in the near future, is expected.

Course Pre-requisites: Basic Molecular Biology, Elementary level Statistics. The participants are also requested to doPractical Introduction to R in advance, ideally just before the course.This tutorial takes less than 30 minutes to follow. To install R locally, go to http://www.r-project.org/ Click on CRAN, select a mirror site and install R locally. It is available for Linux, Microsoft Windows and Apple MacOS X. Links to previous editions: 2009 2008

Application

Detailed Program

Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal GTPB Homepage IGC Homepage Last updated:  July 20th 2010

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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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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

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The unknown future rolls toward us 23andMe, The story continues

The tables turn, it's 23andMe's turn to send a letter to FDA... Continuing the story Reading Between Lines slapped with cease and desist letters.

Direct-to-consumer genomics firm 23andMe has sent a letter to the heads of the US Food and Drug Administration and National Institutes of Health asking for a collaborative effort to develop guidelines for genetic testing.

The firm posted the letter that it sent to FDA Commissioner Margaret Hamburg and NIH Director Francis Collins on its blog, The Spittoon, last night.

23andMe is one of several companies to be targeted recently by FDA, which sent letters to several firms saying that it believes the firms are selling unapproved diagnostic devices. The other firms that received letters were Knome, 23andMe, Decode Genetics, Navigenics, and Illumina, the last of which was cited for providing the tools that are used to provide genetic information to certain of the DTC genomics' customers.

In the letter sent to FDA and NIH, 23andMe noted that there have been reports of inconsistencies in the results provided by DTC genetic test providers. Specifically, it pointed to a paper published in October 2009 in the journal Nature, in which the authors cited inconsistencies in the results provided by 23andMe and Navigenics.

Though Nature did not publish a joint response from 23andMe and Navigenics to that paper, the firms made it publicly available. In that response, they took exception to some of the methods used, but they also said they agreed with most of the recommendations made by the authors, who were from the J. Craig Venter Institute and the Scripps Translational Science Institute.

"We believe that it is important to emphasize that different genetic testing companies can report inconsistent results even when based on tests with proven analytical validity," 23andMe wrote this week in its letter to FDA and NIH. It added that such inconsistent results may be confusing to physicians and consumers alike.

The firm asked FDA and NIH for help in developing broadly applicable standards and guidelines for providing genetic test results and risk estimates. For example, the firm said such a collaborative effort could develop guidelines for acceptable analytical validity; standards for the positive and negative predictive value of tests; and best practices for companies that could lead to results being readily compared across companies.

"We note that any framework developed for genetic testing companies must consider the multiple high throughput technologies on the horizon, including genome, exome and transcriptome sequencing," it said in the letter. "For this reason, the set of ideas we present above does not include having an organization define a specific set of markers as an acceptable genetic test."