Biointelligence

September 11, 2009

List of Companies working on Microarrays and related Data Analysis

Affymetrix —  Developing systems to acquire, analyze and manage genetic info.
Agilent Technologies —   Provider of a range of microarrays for different organisms, manufacture the 2100 bioanalyzer.
Asper Biotechnology —   Manufacture coated microarray glass slides.
Axon Instruments —  Design and manufacture of instrumentation for genomics and proteomics.
BioDiscovery —   Providing software solutions for gene expression research.
BioMicro Systems — Providing the MAUI Hybridization system for active mixing of ultra low volumes during microarray hybridization.
BioRobotics —  Design, manufacture, and supply of automated solutions for molecular biology research.
BioSieve —  Provides microarray data analysis package on Java platform.
Cartesian Technologies —   Providing tools for microscale liquid handling and associated automation.
Clondiag Chip Technologies —  Imaging and LIMS software and technologies.
Clontech — Development and production of innovative biological products.
GeneData —  Providing computational solutions for analyisis of large quantities of data.
GeneLogic — Providing a data management platform for large-scale data analysis.
Genemachines — Developing machinery for genomics automation.
Gene Network Sciences — Developing dynamic computer models of living cells and next generation data-mining tools.
Genomic Solutions — Providing a variety of genomic research tools.
Genetix — Providing microarray printers, scanners, reagents and consumables.
Genotypic — A genomics and bioinformatics company, providing microarray products & services.
Genome Explorations Inc. — Providing Gene Expression analysis using the Affymetrix Platform.
Iobion Informatics LLC —   Microarray data management and analysis software.
LION Bioscience — Providing expression data analysis systems.
Molecular Dynamics —  Developing and manufacturing microarray systems.
Motorola Life Sciences — Developing system solutions for high-performance gene espression profiling.
MWG Biotech — Microarray provider of multiple whole genome arrays, custom arrays and other array products
Ocimum Biosolutions — Providing biotechnology software solutions, including Genowiz for micorarray data analysis and management.
Packard BioScience — Producing tools used in genomics and proteomics.
Perkin Elmer — Providing a list of various microarray products.
Rosetta Inpharmatics — Providers of bioinformatics solutions and gene expression analysis systems.
Scanalytics — Providing image analysis software for extracting and visualizing DNA microarray data.
Silicon Genetics — Providing genomic expression data analysis, visualization, mining, and storage products.
SSI Robotics — Robotic automation systems and instrument integration for life science related processes.
Superarray Bioscience — Developing pathway/application specific gene expression tools

Add more to this list…… !!!

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August 11, 2009

Bioinformatics In Pharma Industry

Bioinformatics provides the computational support for functional genomics which will link the behavior of cells, organism amd population to the information encoded in the genomes, as well as structural genomics. The utility of bioinformatics lies in the identification of useful genes leading to the development of new gene products. The subject covers topics such as protein modeling and sequence alignment, expression data analysis, and comparartive genomics. It combines algorithmic, statistical and database methods for studying biological problems also.

The greatest achievement of bioinformatics methods, the Human Genome Project. Because of this the nature and priorities of bioinformatics research and applications are changing. Many experts believe that this will affect bioinformatics in several ways. For instance some scientists also believe what some people refer to as research or medical informatics, the management of all biomedical experimental data associated with particular molecules or patients – from mass spectroscopy, to in vitro assays to clinical side-effects-move from the concern of those working in drug company and hospital IT (information technology) into the mainstream of cell and molecular biology and migrate from the commercial and clinical to academic sectors.

Drug Development

Only 10% of drug molecules identified in research make it through development. This means that many potential drugs do not make it to market, and expensive time and resources are invested m molecules that will generate no revenue. Simulation and informatics can significantly increase these odds by improving the efficiency of drug development, cutting costs, and improving margins.

Formulation Design

Formulation is the process of mixing Ingredients in such a way as to produce a new or improved product. The formulation department must balance the different marketing and deliverability requirements with cost and chemical constraints to come up with the best possible drug delivery method at the best price. With laboratory results stored in legacy systems, it takes expert company knowledge and experience to know which methods and suppliers are available, let alone to locate them quickly. In many cases scientists find that it is easier to repeat an experiment than to find previous results. This situation is compounded in global R&D set-ups, and after mergers and acquisitions.

Crystallisation and Structure Determination

Determining the crystal structure of an active compound is one of the first steps in pharmaceutical development. The crystal structure of a drug affects how easy it is to formulate, its bio-avail- ability, and its shelf life. Knowledge of the different possible polymorphs of a crystal can also give better patent protection for a drug.

Polymer Modeling

Drug delivery is a complex task. The drug must be delivered in a way that transports the active component intact to the appropriate part of the body. The way the cell takes up the drug is also very important: drugs that go to parts of the body other than the intended target are wasted and may lead to unwanted side effects.

Many delivery devices are polymeric with the drug either solubilised or emulsified in the polymer. Drug delivery systems have mesoscale structures; between 10 to 1000 nm. The amount of computing power required to model these systems at an atomistic level is prohibitive, and macroscale techniques such as Finite element analysis or computational fluid dynamics do not give the required level of detail. Mesoscale modeling, focusing on the nanometer length scale, is helping scientists to develop colloidal delivery systems for drugs.

The great advances in human healthcare that are presaged by the Human Genome Project can be realized by the pharmaceutical industry. A prerequisite for this will be the successful integration of bioinformatics into most aspects of drug discovery. Although, from a scientific viewpoint, this is not a difficult problem, there are formidable technological obstacles. Once these are overcome, rapid progress can be expected.

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 4, 2009

Education in Chemoinformatics

Filed under: Chemoinformatics — Biointelligence: Education,Training & Consultancy Services @ 2:47 am
Tags: , , , ,
Chemoinformatics is rapidly becoming a core part of drug design informatics, yet the educational
opportunities in the field are currently limited.Like many of today’s emerging life science fields, chemoinformatics
has become a ‘hot topic’ while it is still in the process of
finding its identity. Indeed it is not yet clear how to spell the name
of the field: some prefer cheminformatics – no ‘o’ – and others,
including ourselves, use entirely different terms, such as chemical
informatics. What is clear is that the techniques that this field
concerns itself with – the processing of chemical and related
information on computers – are becoming central to the processes
of modern drug discovery.Here

Here is a small post which gives an overview of the current requirements and the courses available in Cheminformatics.

Chemoinformatics is rapidly becoming a core part of drug design informatics, yet the educational opportunities in the field are currently limited.

Like many of today’s emerging life science fields, chemoinformatics has become a ‘hot topic’ while it is still in the process of finding its identity.

Indeed it is not yet clear how to spell the name of the field: some prefer cheminformatics – no ‘o’ – and others, including ourselves, use entirely different terms, such as chemical informatics. What is clear is that the techniques that this field concerns itself with – the processing of chemical and related information on computers – are becoming central to the processes of modern drug discovery.

Interest in chemoinformatics is now becoming widespread, but this greatly increased exposure has highlighted the fact that there are very few people with high-level chemoinformatics skills. The principal source of such individuals in the past has been doctoral students and post-doctoral staff who have spent time in one of the few academic groups world-wide who carry out research in this area, with job opportunities also becoming available to individuals who have worked in areas of chemistry that involve significant computation – such as X-ray crystallography or computational chemistry – or in related areas such as bioinformatics or computational biology. However, there are still too few trained staff available to meet the emerging need, and this has spurred the development of university courses that can provide students with the necessary skills, at both undergraduate and postgraduate levels.

Academic Programs in Chemoinformatics

A small number of universities have established chemoinformatics programs . The most widely recognized and well-established research and teaching base in the field is the Department of Information Studies at the University of Sheffield, which offers Master of science (MSc, or MS) degree and PhD qualifications in chemoinformatics. Subsequent programs have been developed at the University of Manchester Institute of Science and Technology (UMIST), now merged with the University of Manchester, UK, and the School of Informatics at Indiana University (IU), IN, USA.

For a more detailed view refer to the following links:

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.

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.

July 31, 2009

Careers in Bioinformatics

Filed under: Bioinformatics,Systems Biology — Biointelligence: Education,Training & Consultancy Services @ 1:23 pm
Tags: ,

Hey People,

Here is an article on Careers in Bioinformatics. It gives an insight of what actually is required … and how it can be achieved.

Check it out !!


Bioinformatics, the use of computer technology to manage biological information, made its spectacular debut a few years ago, as the first trickles of gene sequence information from the Human Genome Program (HGP) and other sequencing projects grew into a deluge. Individuals with the skills to work on the interface between molecular biology and computer science instantly became some of the most sought-after job applicants in the biopharma world. With about 3 billion base pairs on its agenda, and a target completion date of 2005, HGP alone should foster a continuing explosion of data and a robust job market for computational biologists.
“Career opportunities in bioinformatics are very, very good,” said John M. Greene, senior staff scientist, bioinformatics research, at Gene Logic Inc., Gaithersburg, Maryland. “It seems that every time you turn around a company has decided to set up a bioinformatics group, or expand an existing group. Many scientists are turning their careers in this direction.”
But Greene notes that breaking into the field may not be as simple as all the talk about a feeding frenzy for personnel suggests. He cites the common misperception that a person can take a course in C, the programming language, acquire some database knowledge, and be deluged with high-paying job offers. Salaries around the six-figure mark are possible in bioinformatics, but getting them or even an entry-level position requires more planning than was common in the past.

Not many of today’s bioinformatics people planned it. Many started out doing something else, entered the field before it had a name, and learned key skills on the job. Some were computer scientists who learned biology. Others were life scientists who learned computing.
After getting a Ph.D. in genetics from Harvard University, Greene did a postdoc, and worked for almost a year at a start-up antisense company. His career path led to Human Genome Sciences (HGS) and a job that involved substantial Basic Local Alignment Search Tool (BLAST) analysis on expressed sequence tags (ESTs) to identify genes with possible medical applications. BLAST programs are basic tools for searching DNA and protein databases for sequence similarities. Greene liked the work and finally switched into bioinformatics full time at HGS. He recently moved up to Gene Logic, which offers pharmaceutical companies technology to speed up development of drug targets. Gene Logic has a proprietary technology that identifies changes in gene expression associated with disease. It is developing a flow-through DNA chip to gauge drug efficacy and toxicity by analyzing gene changes, and an object-oriented database of gene expression patterns to identify new drug targets.

Strongest demand today exists for individuals with degrees in the life sciences and computer sciences, and multiple years of programming and database development experience, Greene says. Typical combinations include a Ph.D. in molecular biology, cell biology, or biochemistry and a B.S. in computer sciences. Life science Ph.D’s, largely self-taught in key computer skills, with industry experience, have good opportunities. People who emerge from the few doctoral programs in bioinformatics also will be “incredibly marketable,” especially those with industry experience. This range of individuals, very difficult to find, often wind up heading bioinformatics departments or programs.

At the staff scientist and senior staff scientist levels, biopharma companies now tend to place emphasis on applicants with computer science skills. That’s largely because databases and search tools are still being developed. Greene thinks that emphasis will shift in a few years to interpreting information in databases. Companies will then look for individuals who first and foremost are biologists but have key computational skills.

What are those skills? Greene’s list includes knowledge of UNIX, the operating system used for many computational biology programs; a good grasp of the concept of relational databases, which are the heart of bioinformatics; and skill with Structured Query Language (SQL), a language used to query databases. In the future, knowledge of object-oriented databases may be increasingly important. Programming skills also are essential. Skills with C, the programming language, will help individuals learn Perl, the scripting language widely used in bioinformatics. Object-oriented languages, such as Java, will be increasingly important. Expert knowledge of sequence-analysis programs like BLAST and FASTA is critical. Web skills, of course, are necessary, including the ability to write some Hypertext Markup Language (HTML). What gives one applicant an edge over another? Recruiters get excited over applicants who have applied computational biology skills in a practical way. The individual who wrote a program, for instance, and used it in thesis or postdoctoral work, might have an advantage over a similar individual who just took programming courses.”For individuals who thrill at being on the cutting edge of science, with the skills to excel in two very different worlds, bioinformatics can be an extraordinarily good career,” Greene said. “For me, the switch was the best step I’ve taken in the last decade.”