Biointelligence

August 11, 2009

EMBRACE – Active registry for bioinformatics web services

Filed under: Bioinformatics — Biointelligence: Education,Training & Consultancy Services @ 12:47 pm
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Web services’ have become important tools in bioinformatics, allowing databases and algorithms to be accessed programmatically as computational components in programs, workflows and interactive analysis tools. Although these services are becoming common, with an growing adoption of standard protocols and technologies, the mechanisms for collecting and publicizing them are less mature.
A number of mechanisms for finding services have emerged over recent years but they have various limitations.

The EMBRACE (A European Model for Bioinformatics Research and Community Education) Network of Excellence has produced a web service registry that attempts to tackle the limitations and drawbacks of the already existing systems.The EMBRACE Service Registry is a collection of life-science web services with built-in service testing.

The EMBRACE registry is a collection of life-science web services originating from the EMBRACE Network of Excellence. As a potential user of these, you can search the registry for services that match your needs, and find example client software to help you use them in your own programs or workflows. The registry periodically monitors the status and behaviour of the registered services, collating and logging this information so that you can see how reliable services are, and whether they are currently functioning as the service providers expect them to.

To access EMBRACE click on the following link – http://www.embraceregistry.net/

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August 5, 2009

Bioinformatics Companies

Here is a list of Bioinformatics Companies worldwide. Would be soon posting on companies working in specialised areas of bioinformatics.


List of Bioinformatics Companies World Wide

Australia

  1. Nucleics
  2. Australian Genome Research Facility
  3. IBM Healthcare and Life Sciences
  4. CSIRO Bioinformatics
  5. Minomic
  6. Proteome Systems

Austria

  1. ProCeryon Biosciences GmbH
  2. Lambda Labor für Molekularbiologische DNA-Analysen GmbH
  3. Upper Austria Research
  4. DSM fine Chemicals Austria
  5. Pfitzer
  6. ARC Seibersdorf Research GmbH
  7. Roche Austria
  8. CD Labor f. Genomik und Bioinformatik
  9. Gen-au, Genomforschung Austria
  10. Inte:Ligand

Belgium

  1. Algonomics
  2. Bayer Bioscience
  3. BioXpr – computer science & molecular biology
  4. Tibotec
  5. VircoLab
  6. Biodata
  7. Applied Maths

Canada

  1. Caprion Proteomics
  2. Zymeworks
  3. BioMolTech
  4. Biotools Inc
  5. Molecular Mining Corporation
  6. Base4 Bioinformatics Inc.
  7. Bioinformatics Solutions
  8. Chemical Computing Group

Denmark

  1. CLC Bio
  2. Bioinformatics ApS

Finland

  1. Genolyze Ltd

France

  1. Partner Chip
  2. BioSolution
  3. Korilog

Germany

  1. Cubic Design
  2. Biomax Informatics
  3. BIOBASE Biological databases

IceLand

  1. deCODEme

India

  1. HH Biotechnologies
  2. BIOBASE Biological Databases
  3. Astrazeneca
  4. Avesthagen
  5. Cell Lines
  6. Monsanto
  7. INFOVALLEY Biosystem India Pvt Ltd
  8. Strand Life Sciences (formerly Strand Genomics)
  9. Connexios Life Sciences Pvt. Ltd.
  10. GVK Biosciences Pvt Ltd
  11. IBM Life Sciences
  12. Metahelix Life Sciences Pvt Ltd
  13. Biocon, Ltd
  14. Genbios
  15. BioCOS Life Sciences
  16. Jubilant Biosys
  17. Jigsaw Bio Solutions
  18. Nectar Lifesciences Ltd
  19. Orchid Chemicals & Pharmaceuticals Ltd
  20. Neozene Bio Sciences
  21. Neogen Biosolutions
  22. ATGC Labs
  23. Ranbaxy Laboratories Limited
  24. TATA Consultancy Service
  25. Ocimum Biosolutions
  26. Dr.Reddy’s Pharmaceutical Company
  27. BioMinds Life Sciences Pvt. Ltd
  28. BioMed Informatics
  29. Ingenovis
  30. GlaxoSmithKline Pharmaceuticals Ltd.
  31. Sun Pharmaceutical Industries Ltd
  32. Rishi Biotech
  33. C-DAC: Centre for Development of Advanced Computing
  34. SooryaKiran Bioinformatics

Ireland

  1. SlidePath

Israel

  1. Evogene Ltd
  2. Compugen
  3. Optimata

Italy

  1. ICGEB

Malaysia

  1. Synamatix

New Zealand

  1. Biomatters
  2. Hoare Research Software
  3. HortResearch

Norway

  1. Interagon
  2. MolMine
  3. PubGene
  4. Sencel Bioinformatics

Russia

  1. GeneGo

Singapore

  1. Lilly Singapore Centre for Drug Discovery

South Africa

  1. ICGEB

Spain

  1. Integromics™ | IT for Life Sciences
  2. Bioalma
  3. Ariadne Genomics Europe

Sweden

  1. Qlucore
  2. Agile Molecule

Switzerland

  1. Merck Serono International
  2. Detectorvision
  3. Genedata
  4. Geneva Bioinformatics(GeneBio)

United Kingdom

  1. Astex Technology
  2. ePitope Informatics Ltd
  3. InfoQuant
  4. SimuGen
  5. ProGeniq
  6. BlueGnome
  7. etrials
  8. IDBS
  9. InforSense
  10. Matrix Science

United States of America

  1. 23andme
  2. Accelrys
  3. Navigenics
  4. Rosetta Biosoftware
  5. GeneSifter
  6. Seralogix
  7. Ariadne Genomics
  8. ATGCLabs
  9. BioAnalytics Group
  10. Bio-Rad
  11. Geospiza
  12. VigeneTech
  13. Allometra
  14. Ariadne Genomics
  15. Axcell
  16. Biodiscovery
  17. Biopharm Systems
  18. Biotique Systems
  19. BioWisdom
  20. Cellnomica
  21. Cira Discovery Sciences
  22. Cognia
  23. IBM (Bioinformatics and Pattern Discovery Group)
  24. Ocimum Biosolutions

Please keep adding if you are know a company working in this stream !!

August 3, 2009

Bioinformatics: Mining for Jobs

Filed under: Bioinformatics,Computational Biology — Biointelligence: Education,Training & Consultancy Services @ 4:54 pm
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The growing number of courses and experienced workers in bioinformatics points that the recruitment market has become tougher for new buds.

The publication of the draft sequence of the human genome in 2001 was not only a monumental achievement in science but also signalled the future of bioinformatics. With information on gene expression, protein structure and function, and disease susceptibility being applied to the genome sequence, pharmaceutical companies needed the right tools and expertise to make sense of the deluge of data spewing out of laboratories.

Early on, recruited staff usually fell into two groups: biologists who had some computer skills or computer scientists who had some knowledge of biology. In general, companies tended to favour the former.

“Bioinformaticians need to understand computer languages, but a fundamental and thorough understanding of biology is crucial in making sense of biological data and extracting the meaningful information.”

Bioinformatics requires different skills at different stages. These have been reperesented using the flow chart.

Skills required in bioinformatics at different stages

Bioinformatics has become sensitive to market trends. In recent years, companies have come and gone, such as Oakland, California-based Double Twist in 2002. Many leaders in the field, such as Celera and Incyte, have changed their business models from pure informatics-based approaches to applied approaches. Some companies recommend that if you really want a career in bioinformatics, doing a Ph.D. on a relevant project will provide you with experience, and having high-quality publications will strengthen your CV. Another way of gaining experience is to analyse the many data sets that are available on the Internet, such as gene-expression data from microarrays.

Bioinformatics is still a rapidly growing field. Large pharmaceutical companies are relying on informatics to improve efficiency, to allow more rapid decision making around existing projects and to more readily identify new ideas and targets. New areas, such as systems biology, will, if embraced by industry as anticipated, also require the skills of bioinformaticians. Mining for the right background and experience will increase your chances of joining this hottest of fields.

August 1, 2009

Widening Horizons in Bioinformatics

Filed under: Bioinformatics — Biointelligence: Education,Training & Consultancy Services @ 1:47 am
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In my previous post, we read about various career opportunities in Bioinformatics…. but what is the actual work done in the industry. Here is my next post which talks about it.


With genomics research making strides, the volume of life sciences related data is increasing at a very fast pace. Organizing, analyzing and further utilizing this knowledge, collectively called as bioinformatics, is still a nascent and largely unexplored field in India.

With the global bioinformatics segment expected to grow to $6 billion by 2005 according to several studies, opportunities abound in this sector. The fact that in the next 10 years most new drug designs will be genomics-related and there being a global shortage of one million professionals in this field, this unique niche area is waiting to be explored. Though the opportunity exists, it should not be construed that bioinformatics is the next big thing. It is not and cannot be compared with the IT sector say industry observers.

“There is a lot of data to be managed and mined. However, biotech companies over the last two years have been busy surviving and had not looked at solution providers for informatics solutions in a big way. Pharma companies, on the other hand, look for ready products to be bought and are generally averse to outsource custom projects. Availability of free software or software bundled with analytical equipment is another challenge facing the pure play bioinformatics companies,” pointed Ajay Simha, director, SysArris Software Pvt Ltd, a Bangalore based company offering IT software solutions and services to the pharma and biotech segment since the past eight years.

Vibhav Garg, functional consultant, Mascon Life Sciences, a New Delhi based company that develops bioinformatics software for pharma companies and research labs, feels that the current buzz about bioinformatics is partially justified. “There is an urgent need to understand the available data. But the hype created by unauthorized so-called training centers is absolutely unwarranted and many times creates confusion in the minds of new entrants,” Garg informed.

None deny that bioinformatics, the amalgamation of biology and information technology, requires a range of “interdisciplinary skills”. “The requirement here is to be able to have a good blend of computer and life science scientists working together and delivering solutions, which are the best of both domains. This is so because it combines two domains with very different principles and ways of functioning,” observed S Sowmyanarayan, manager, business development and alliances of Strand Genomics, Bangalore.

Bioinformatics companies generally have well-defined teams with a clear business focus. For example, in Mascon, there are three groups—a functional team, which is the driving force, consists of domain experts. The development team is the supporting arm and comprises the software professionals. Then there is a business development team. Likewise, SysArris has domain experts who are thorough in genomics, cheminformatics and other areas. These experts understand the requirements of customers, analyze it and suggest the solution. The software team then converts the requirements to a software solution.

Till last year, bioinformatics accounted for about 4 percent of the total size of the biotech industry, but it is expected to catch up fast. The total sales revenue (2002-03) generated by this segment was about Rs 75 crore and a major chunk of it (64 percent) was through projects for overseas companies. Today most of the companies in this segment are small to mid size, with employees ranging from 25 to 200 plus and the average man to women ratio is 2:1.

The salary range depends on the experience and capabilities of the person and performers are recognized and well rewarded. “While the starting salaries could be anywhere from Rs 10,000 to Rs 20,000 per month depending on the experience of the candidate, it can go up very high as there is a review every six months,” said Anuradha Acharya, CEO, Ocimum Biosolutions, Hyderabad. Others too feel the same. The salaries offered can start from Rs 1.8-2 lakh per annum and can reach as high as Rs 12-15 lakh per annum based on the experience and type of skills.

This nascent field provides immense growth opportunities in terms of knowledge base, market exposure and career advancement. “We have identified several growth tracks for our employees. These could be either in pure software development, bioinformatics, management or sales and marketing. A person could start as a trainee, bioinformatician or software developer and could end up becoming part of the top management,” added Anuradha.

Selection process

For entry and junior level candidates, companies conduct written tests and interviews, whereas at senior levels intake is generally through referrals and a round of discussions. “We generally look for people with at least one year relevant experience; if no suitable candidates are found, we take the most suitable candidate and train on-the-job,” said Ajay Simha. Some of the companies do campus recruitments. Often, companies prefer to go to the IITs and RECs.

Most companies have a very structured procedure for intake of candidates. Like Anuradha Acharya explained, “The procedure for manpower selection starts with management review meeting where the resource plan for manpower recruitment is prepared. After the resource plan is prepared, the next step is to find out the reliable resources to get the manpower. For instance registration with the jobsites, placing an advertisement in paper, approaching consultants and through employee referral program, which is called ‘Introcentive’. The next step is scanning resumes for a specific requirement and short-listing them. Then the short listed candidates have to go through a screening test. After qualifying the screening test, an applicant has to undergo a minimum of three rounds of interview. Once the applicant is through with all the above rounds, he/she would be put to the top management for final interview. Once the top management is convinced, the next step would be issuance of an offer letter.”

Besides the basic qualification (a masters or higher degree in a branch of life science or computer science), prior experience or training in the industry or research organization is an added advantage concur most company heads. But the experience required would depend on the openings from time to time. As such, bioinformatics being a new field, it is very difficult to get people who have cross-functional expertise. Hence, the companies generally provide training before putting the candidate to work. Some like Ocimum Biosolutions offer a postgraduate diploma program in bioinformatics in association with University of Alabama at Huntsville. The duration of the course is six months. The students who join this program usually have expertise or a degree in either life sciences or computer science. The program nurtures them to become cross-trained. “This has worked out very well for Ocimum both in terms of recruitment and also keeping the development team up to date with the subject. All employees are also encouraged to participate in this program,” elaborated Anuradha. Many bioinformatics companies have an arrangement for short-duration high-end specialized training for working professionals. They permit internship projects for students.

According to YK Maheshwari, Sr VP, health care and life sciences, Kshema Technologies, Bangalore, “Hands-on training or experience is not a necessary prerequisite, but those with such experience are obviously preferred. Selection is easier for engineers or professionals, who have developed software, who understand the development SDLC (Life cycle processes) and know the requirement gathering process or candidates with knowledge on data warehousing, business intelligence, pharma workflow, lab management systems, FDA approval process, drug discovery life cycle”.

So is there a future? Maheshwari summed up: “There are multiple opportunities, in what goes under the wide banner of bioinformatics. Technical developments such as molecular genetics, proteomics and metabolomics provide the analytical base to support the advances in life sciences, but there is a demand for novel automated tools to reduce the time involved in the discovery life cycle. There is a shortage of individuals, though critical for the future, with the necessary multidisciplinary expertise for the development of genomic/analytics applications that demands a high level of knowledge/interpretation skill beyond that previously employed in the information technology sector.”

But at the same time the buzz about bioinformatics is not entirely justified since it undermines the requirement of core strengths such as fundamental biology, genetics, molecular biology, statistics, computer science and mathematics and places emphasis instead on a loose mix of all these fields.