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.

Proteomics: Challenges and Approaches

Filed under: Bioinformatics,Proteomics — Biointelligence: Education,Training & Consultancy Services @ 9:05 am
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Proteomics is the study of the function of all expressed proteins. The term proteome was first coined to describe the set of proteins encoded by the genome1. The study of the proteome, called proteomics, now evokes not only all the proteins in any given cell, but also the set of all protein isoforms and modifications, the interactions between them, the structural description of proteins and their higher-order complexes, and for that matter almost everything ‘post-genomic’. In this overview we will use proteomics in an overall sense to mean protein biochemistry on an unprecedented, high-throughput scale.

Proteomics complements other functional genomics approaches, including microarray-based expression profiles, systematic phenotypic profiles at the cell and organism level, systematic genetics and small-molecule-based arrays. Integration of these data sets through bioinformatics will yield a comprehensive database of gene function that will serve as a powerful reference of protein properties and functions, and a useful tool for the individual researcher to both build and test hypotheses. Moreover,this large-scale data sets will be of utmost importance for the emerging field of systems biology.

Platforms for Proteomics 

Challenges and Approaches in Proteomics

Proteomics would not be possible without the previous achievements of genomics, which provided the ‘blueprint’ of possible gene products that are the focal point of proteomics studies. Some of the recent approaches used in the field of proteomics are:

1. Mass spectrometry-based proteomics

2. Array Based Proteomics

3. Structural Proteomics

4. Proteome informatics

5. Clinical Proteomics

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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.