Biointelligence

August 14, 2009

Python for Biologists

Filed under: Bioinformatics,Computational Biology — Biointelligence: Education,Training & Consultancy Services @ 3:27 pm
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While reading through a PLOS journal, found an article on the importance of Python for Life Science Researchers.

An article written by Sebastian Bassi, gave a proper insight of what is Python and how it can be of great use for the Life Science Research Community. Here is a summary of that article.


Python is a modern programming language developed in the early 1990s. It is a dynamic high-level language with an easily readable syntax. Python programs are interpreted, meaning that there is no need for compilation into a binary form before executing the programs. This makes Python programs a little slower than programs written in a compiled language, but at current computer speeds and for most tasks this is not an issue and the portability that Python gains as a result of being interpreted is a worthwhile tradeoff.

Basically, this language is easy to learn, easy to read, interpret and multiplatform. Its simplicity is a design choice, made in order to facilitate the learning and use of the language. Another advantage well-suited to newcomers is the optional interactive mode that gives immediate feedback of each statement.

Python can be used to solve several problems that research laboratories face almost everyday. Data manipulation, biological data retrieval and parsing, automation, and simulation of biological problems are some of the tasks that can be performed in an effective way with computers and a suitable programming language.

For a detailed information on python click the link below:

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0030199

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

Careers and Opportunities in Chemoinformatics

Filed under: Bioinformatics,Chemoinformatics — Biointelligence: Education,Training & Consultancy Services @ 2:56 am
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After Bioinformatics the next new buzz is Chemoinformatics.. but what is it. Here is an article which I found.


When two scientific disciplines meet, they can be mutually beneficial, fill each other’s voids – and complement each other, giving rise to unprecedented scientific opportunities. One such field of recent interest is chemoinformatics. Chemoinformatics plays a key role in areas as diverse as chemical genomics and drug discovery, the storage of chemical information in databases and the prediction of toxic substances. Today, these techniques are mostly used in pharmaceutical companies in the process of drug discovery, but also for example in “functional foods”, designed by nutritional companies to improve body functions, such as for example digestion or brain function.

While bioinformatics is known since 1976 which is defined as “the study of informatics process in biotic systems”, the emerging terminology in the pharmaceutical sector is commonly referred to as chemoinformatics, which is defined as the “mixing of information resources to transform data into information and information into knowledge, intending for better rapid decisions in the arena of drug lead identification and optimization”.

Chemoinformatics is a generic term that encompasses the design, creation, organization, storage, management, retrieval, analysis, dissemination, visualization and the use of chemical information – so, virtually every area where “chemical data” is accessed or changed by means of computers. Chemoinformatics represents a vital link between experiment and theory in the area of drug design, through the extraction of information from data and conversion into knowledge. With the explosion of publicly available genomic information, such as that resulting from the Human Genome Project, in the middle of the 1990s, bioinformatics has become very popular not only in the scientific community but also among the general audience. This has led to the coining of the counterpart of bioinformatics in chemistry after about two decades as Chemoinformatics. However this field can actually be seen as about two hundred years old – ever since the first account of chemical data has been published in literature.

Today’s technology in chemoinformatics in fact facilitates better organization, storage, retrieval and analysis of these data for further advanced predicting studies – thus, saving time and money, also possibly animal experiments, and advancing humankind by developing novel, and safer, drugs. The last three decades have seen tremendous growth in this field with the advancement in the computer technologies. Today volumes and volumes of books has been written on this subject and even few text books available for teaching in universities at the BSc and MSc level. Though there are full time Masters degree programs available in universities abroad, in India this field has yet to get full recognition.

Currently chemoinformatics is being introduced as part of an ongoing diploma or masters program in bioinformatics in spite of its maturity as a new discipline. Besides the traditional mainstream areas of chemoinformatics such as database systems, computer-assisted structure elucidation systems, computer-assisted synthesis design systems, and quantitative structure-activity relationship (QSAR), several new research areas of chemoinformatics have appeared recently, such as in silico library design, virtual screening, docking, prediction of ADME (Absorption, distribution, metabolism and excretion) and toxicity. It is interesting to notice that at the end of 20th century almost all the major foundations and theories of chemistry had been well understood and established. Chemistry has already evolved from largely a study of the elements to a study of molecules to currently a study of molecular interactions, especially those involving biological macromolecules – the molecules such as proteins and sugars we humans are made of.

This offers a excellent opportunity for chemoinformatics to grow in this new direction. The main focus of recently identified “cyber enabled chemistry” by the US National Science Foundation is on the development of integrated databases, data mining tools, molecular visualization and computational capabilities and the remote and networked use of instrumentation. The scope of this rapidly developing field will certainly continue to expand. It is worth mentioning that there is a new trend of integration of chemoinformatics with bioinformatics. This is because many sectors of the chemical and pharmaceutical industries are interdisciplinary by nature, and major progress and developments in those industries are occurring in both bioinformatics and chemoinformatics side by side. Chemists will become more and more computer dependent, Internet dependent and chemoinformatics dependent. Chemoinformatics through its development in the past half a century, has reached in the present wide acceptance, and will have a bright future!

The purpose of this particular article is to highlight the various research and job opportunities available to a new generation of students in chemistry, computer science and biology at various levels in both academic and pharmaceutical environment.

Job Title of Recent Graduates

Graduates from the MSc in Chemoinformatics have taken up a variety of different types of posts upon starting employment. Examples of the job titles of recent graduates are given below: Chemoinformatics Scientist, Computational Chemist, Chemical Data Scientist, Regulatory Affairs Officer, Senior Information Analyst, Information Officer, Data Officer, Graduate IT Trainee, Programmer, QSAR Software Tester, Support Analyst, Business Analyst, Technical Editor, Consultant, Research Assistant  Organizations/Companies of Recent Graduates etc.,

Graduates from the MSc in Chemoinformatics obtain posts with a wide range of organizations and companies. Some of the companies sponsoring chemoinformatics products and activities include: Abbott Laboratories, AstraZeneca, Advanced Chemistry Development, Accelrys, Chemical Computing Group, Barnard Chemical Information Ltd., Beilstein, Jubilant Biosys, Johnson & Johnson, Lilly, Lupin, General Electrics, GlaxoSmithKline, Hoffman La Roche, Novartis, Molecular Design Limited, Merck, Pfizer, Proctor and Gamble, Ranbaxy, Tripos, Unilever, Wyeth etc.,

Some of the research laboratories / Universities / Not for profit organizations actively involved in chemoinformatics activities include: National Chemical Laboratory-Pune, CDRI-Lucknow, RRL-Jammu, Indian Institute of Technology (Delhi), Indian Institute of Science, University of Leeds (UK), Royal Society of Chemistry, University of Sheffield (UK), University of Erlangen (Germany), University of North Carolina (USA), Pune University (India), Chemical Abstract Service (American Chemical Society, USA) etc.

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.

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