Bio Saga Headlines

Bio Saga

Wednesday, April 30, 2008

British Team Finds Two Genes For Osteoporosis

British researchers have identified two common genetic mutations that increase the risk of osteoporosis and related bone fractures, according to a study released on Tuesday. These changes were present in 20 percent of the people studied and highlight the potential role of screening for the bone-thinning.

Talking about Osteoporosis, other related bone diseases affecting bone formation and repair. There has been increased interest both in academia and industry in tissue regeneration and working towards understanding the biological processes involved in self regeneration.

The key to success is in understanding basic developmental processes focused on tissue regeneration (including bone formation and repair). One such key resource researchers might be interested in, is Receptome a knowledgebase of functional endogenous ligand-receptor pairs in developmental processes.

Few key applications areas are : to identify major mediators, roles in cellular processes, expression and role of specific cell surface receptors, multi-receptor pharmacology, identify high affinity ligands and activators, natural modulators of functional ligand-receptor pairs, critical signaling nodes, transcription factors, target genes, etc.

Tissue-specific blood stem cell line established from embryonic stem cells

A research team at the Umeå Center for Molecular Medicine (UCMM) in Sweden, led by Professor Leif Carlsson, has managed to specifically establish and isolate the tissue-specific stem cell that produces blood cells (blood stem cell) by using genetically modified embryonic stem cells.

to know more

Yet another challenge to informatics, well does it have the answer this time?

Among number of challenges faced by informatics one of the long standing and critical challenge has been the Biodiversity informatics: the challenge of linking data and the role of shared identifiers.

A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers [such as Digital Object Identifiers (DOIs) and Life Science Identifiers (LSIDs)], and the implementation of services that link those identifiers.

Tuesday, April 29, 2008

Nature News catches up on the state of gene therapy trials against blindness

Blogging already on the recent developments in Gene Therapy , This weekend two teams reported success in helping people to see again. Nature News catches up on the state of gene therapy trials against blindness due to Leber’s congenital amaurosis (LCA).

LCA, a rare inherited form of blindness. Patients with LCA have a genetic defect that affects the development of the light receptors in their eyes; typically they have poor vision at birth and are blind within three decades. Some 3,000 people are thought to be affected in the United States.

here are answers to some important questions that may arise like:

What sort of blindness do the new reports address?

Were the patients 'cured'?

How does it work?

What other treatments are being investigated for severe blindness?

Has gene therapy been trialled for blindness before?

for answers read


A price tag of around US$1 billion to map human proteome

Ambitious plans to catalogue and characterize all proteins in the human body — a Human Proteome Project — are being drawn up by a small group of researchers. But with a price tag of around US$1 billion, some question whether the organizers can raise enough money or momentum for such an undertaking.

Project aims to characterize all human proteins. Talking about characterizing human proteins; there are several organizations working around the globe towards this initiative, spanning across both the public and commercial domains. Having missed out on HGMP, this time the industry in India is all geared up towards the mapping of human proteome.

Molecular Connections collaborates with Plasma Proteome Institute and with Max Planck Institute of Psychiatry, Proteomics & Biomarkers Research Group that would significantly aid them in the development of their new knowledgebase CliPro.

Beating heart tissue grown in lab

Talking about novel receptor genes expressed in human tissues. This morning's news featured, An international team of cell biologists has created heart tissue — complete with beat — in a test tube. The tissue culture contains three distinct cell types, each of which is important in functioning hearts, and is thus a step towards the advent of lab-grown heart-tissue transplants.

To day, research is considerably accelerated by the use of scientific knowledgebase and informatics tools which aid researchers significantly minimize time and effort spent on knowledge transfer across their teams and in scientific study. Thanks to such tools which supplement lab work and act as comprehensive repertoire that make optimal use of the plethora of data available in literature and centralize it as a searchable tool to investigate the characteristics of functional ligand-receptor pairs and their potential use and applications.

The research team led by Gordon Keller of the McEwen Centre for Regenerative Medicine in Toronto, Canada, created the heart cells from human embryonic stem cells. Researchers found that treating the embryonic stem cells with growth factors encourage them to develop into cardiovascular progenitor cells which have the potential to become any of three specialized types of heart cell — two muscle cell types (cardiomyocytes and vascular smooth muscle) and endothelial cells.

When these progenitor cells were grown in a dish, they developed their own intrinsic 'heartbeat'. What's more, when researchers transplanted a mixture of the three cell types into the hearts of mice with simulated heart disease, their heart function improved significantly. Although not yet tested in humans, the technique could offer a useful way to patch up heart muscle damaged by a heart attack.

Monday, April 28, 2008

Gene therapy success 'reverses' blindness





Experimental gene therapy trials have improved the vision of four people who suffer from hereditary blindness.

The preliminary results of two independent studies suggest that "repair" genes delivered to the eye might one day cure Leber congenital amaurosis (LCA), a rare disease that strikes about 1 in 80,000 people in the UK, and 2,000 Americans in total.

Equally important, say researchers, the treatments proved safe in the six patients who received the genes – delivered by a disabled virus – via eye surgery.

"This is really an exciting result for gene therapy as a field," says Katherine High, of the University of Pennsylvania Medical School in Philadelphia, who was part of an international team that presented the findings at a conference yesterday.

Another team led by Robin Ali, of University College London, presented similar results.

read full report

see what BBC reports

Phylogenetics Support Tyrannosaurus Rex's Evolutionary Relationship with Birds

Tyrannosaurus rex peptide sequences are more similar to modern-day birds than to reptiles, according to new research, providing added evidence for a relatively close evolutionary relationship between dinosaurs and birds.

About a year ago, researchers from Harvard University and elsewhere first reported that they could tease minuscule amounts of protein from mastodon and T. rex bone samples that were up to 600,000 and 68 million-years-old, respectively, and analyze them by mass spectrometry.
Now, members of the same team report using molecular phylogenetics to group mastodon and T. rex based on their collagen protein peptide sequences. These latest results, appearing in today’s issue of Science, suggest T. rex is more closely related to chickens and ostriches than to alligators and seem to confirm the long-held suspicion that dinosaurs and birds have a common ancestor. They also corroborate a relationship between mastodons and modern day elephants.

for more

Friday, April 25, 2008

New Molecule Could Be Key To Anti-heart Attack Drug

Heart attacks are commonly caused by blood clots formed of blood platelets. A new research suggests that it should be possible to create a clot-busting pill that targets a receptor on the blood cells’ surface, something that high-risk patients could take at the first sign of chest pain.

The key to such a pill is according to the research findings a receptor called αIIbβ3 on the platelets’ surface that is intimately involved in the aggregation process. Interfering with αIIbβ3 can prevent an unwanted thrombus and the three αIIbβ3 inhibitors currently on the market can do just that. But they also have side effects and risks and must be administered intravenously. Researchers at Rockefeller University have found a new molecule, called RUC-1, that not only appears to sidestep these problems but, unlike existing drugs, could be taken orally.

Molecular Connections Pvt. Ltd. to Sponsor ICIC for the second time

The International Conference in Trends for Scientific Information Professionals

Habitual attendees say that "it is the meeting to which they go to spot the trends, as well as the meeting that provides unparalleled opportunities for networking" Trends and networking will be high on the Nice agenda in October 2008.

The ICIC meeting covers trends in the field of scientific and professional information with an impressive line-up of significant figures in the information world. Among the topics that will be covered and discussed by the 22+ speakers are:

  • Tools for Competitive Intelligence (e.g., mining tools, visualisation tools, analysis tools, etc)
  • Challenges for the information community over the next five years
  • Changes in the information environment for patents, innovation and intellectual property
  • Trends in Search Engines and Information Retrieval (also see)
  • Case Studies in Data and Content Integration

Dawn of the GATTACA era!

The Genetics Information and NonDiscrimination Act passed unanimously today. GINA has sowed the seeds for... I am sure that every one remembers Gattaca 1997 SiFi flick. A genetically inferior man assumes the identity of a superior one in order to pursue his lifelong dream of space travel. During this time society analyzes your DNA and determines where you belong in life. Vincent the protagonist is one of the last "natural" babies born into a sterile, genetically-enhanced world, where life expectancy and disease likelihood are ascertained at birth.

The Gattaca era is now here we are living it, the Genome enters your drawing room of your very home, and people can exchange their gene cards with your medical practitioners. May be very soon even sit at a fertility clinic and discuss the traits of your to be new born. Now the Genome enters the White House oval office too Avatar GINA!

What is the Genetic Information Nondiscrimination Act?

The Genetic Information Nondiscrimination Act [H.R. 493, S. 358] is a bill that will prohibit discrimination on the basis of genetic information with respect to health insurance and employment. It was introduced to establish basic legal protections that will enable and encourage individuals to take advantage of genetic screening, counseling, testing, and new therapies that will result from the scientific advances in the field of genetics. It would also prevent health insurers from denying coverage or adjusting premiums based on an individual's predisposition to a genetic condition, and prohibit employers from discriminating on the basis of predictive genetic information. Additionally, such legislation would stop both employers and insurers from requiring applicants to submit to genetic tests, maintain strict use and disclosure requirements of genetic test information, and impose penalties against employers and insurers who violate these provisions.

Well no one can stop the flow of the wild river that is technology it is always a double edged sword. While GINA is a boon to all the enterprise both commercial and non-profit dealing with personal genomics and genetic testing & patient care. It has opened the flood gates to...?

New Social competition, may be even a new social order!

The world needs Jest Technocrats and Scientist with Human Values to save humanity form Dr.Frankenstein and Dr. Jekyll & Hyde. It is high time the world politics is lead by scientists and not by mad men and power mongers and "Politicians"!


Thursday, April 24, 2008

Structured Digital Abstracts - Easier Literature Searching

Already blogging on similar lines and the subject of Bring in data from the published literature in my earlier blog Smart tools to track, analyze and visualize research , here is another interesting experiment on similar lines:

The experiment centres on Structured Digital Abstracts (SDA). SDA are extensions of the normal journal article abstracts that describe the relationship between two biological entities, mentioning the method used to study the relationship. Each sentence is preceded by one or more identifiers pointing to the corresponding database entries that contain the full details of the interaction e.g. protein A interacts with protein B, by method X.

The aim of SDA is to assist data entry, text mining and literature searching by extracting the salient data from the article into simple sentences using a defined structure and controlled vocabularies.

Gianni Cesareni, Editor of FEBS Letters explains:

Many articles in biological journals describe relationships between entities (genes, proteins, etc.) yet this information cannot be efficiently used because of difficulties in retrieving from text. Databases capture this valuable information and organize it in a structured format ready for automatic analysis. The experiment of using SDAs will facilitate database entry and improve disclosure, to the benefit of authors and readers.


What makes the sequencing of Watson's genome different from that of Venter's?

It's the technology. Watson's genome was sequenced using one of the next generation sequencing technologies (454), which allows much more sequencing bang for the buck. This isn't a $1000 genome, but it's a step in that direction. The real value of Watson's genome sequence is a proof of principle. This project was completed at a low cost (relative to the previous methods of sequencing genome), but with high quality. They were able to identify not only sequence variation between Watson and the reference genomes, but also structural variation. To truly realize the potentials of personal genomics, we need many more of these genomes, with the phenotypic data on the individuals.

Along with the article, Nature has published a News and Views piece on the Watson genome paper. The article takes many steps to point out that, while we are at the cusp of an era of personal genomics, there are many limitations as to what we can do with these data. Given our current knowledge, we can't say much about Watson's phenotype that we didn't already know based on non-genomic information. Personal genomics needs not only data, but also ways of assigning genomic variants to particular phenotypes. At this point, we're probably limited to advising a couple about the risks that their child will acquire a particular genetic disease based on sequencing of the mother and father's genomes.

Wednesday, April 23, 2008

Amazon Molly on Eolution@Home

Scientists at Edinburgh University have been studying complex mathematical models on a highly powerful computing system to look at the case of the Amazon Molly. Researchers calculated the time to extinction for the fish based on modelling genetic changes over many thousands of generations. They are now able to say conclusively, for the first time, the fish ought to have become extinct within the past 70,000 years, based on the current simple models.

Evolution@home is the first global computing system for evolutionary biology. It allows everybody with an Internet PC to contribute to evolutionary-research by running simulations of evolution.
The research is published in the journal BMC Evolutionary Biology.

and the News is on BBC too



Computational chemistry is now, any child's play!

"SimBioSys, announces that their 'eHITS Lightning' program Redefines the State-of-the-art for Structure-Based Virtual Screening" Also have successfully tested and run, eHiTS lightning on a Sony Playstation3. Isn't that amazing!

PlayStations to support computational chemistry

An ontology that bridge biological and computational spheres in bioinformatics

IMGT®, the international ImMunoGeneTics information system (http://imgt.cines.fr), is the reference in immunogenetics and immunoinformatics. IMGT standardizes and manages the complex immunogenetic data that include the immunoglobulins (IG) or antibodies, the T cell receptors (TR), the major histocompatibility complex (MHC) and the related proteins of the immune system (RPI), which belong to the immunoglobulin superfamily (IgSF) and the MHC superfamily (MhcSF). The accuracy and consistency of IMGT data and the coherence between the different IMGT components (databases, tools and Web resources) are based on IMGT-ONTOLOGY, the first ontology for immunogenetics and immunoinformatics.

IMGT-ONTOLOGY manages the immunogenetics knowledge through diverse facets relying on seven axioms, ‘IDENTIFICATION’, ‘DESCRIPTION’, ‘CLASSIFICATION’, ‘NUMEROTATION’, ‘LOCALIZATION’, ‘ORIENTATION’ and ‘OBTENTION’, that postulate that objects, processes and relations have to be identified, described, classified, numerotated, localized, orientated, and that the way they are obtained has to be determined. These axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope.

These axioms have been essential for the conceptualization of the molecular immunogenetics knowledge and for the creation of IMGT. Indeed all the components of the IMGT integrated system have been developed, based on standardized concepts and relations, thus allowing IMGT to bridge biological and computational spheres in bioinformatics. The same axioms can be used to generate concepts for multi-scale level approaches at the molecule, cell, tissue, organ, organism or population level, emphasizing the generalization of the application domain. In that way the Formal IMGT-ONTOLOGY represents a paradigm for the elaboration of ontologies in system biology.

for more

Protein structure databases with new web services for structural biology and biomedical research

The Protein Data Bank Japan (PDBj) curates, edits and distributes protein structural data as a member of the worldwide Protein Data Bank (wwPDB) and currently processes ~25–30% of all deposited data in the world. Structural information is enhanced by the addition of biological and biochemical functional data as well as experimental details extracted from the literature and other databases. Several applications have been developed at PDBj for structural biology and biomedical studies: (i) a Java-based molecular graphics viewer, jV; (ii) display of electron density maps for the evaluation of structure quality; (iii) an extensive database of molecular surfaces for functional sites, eF-site, as well as a search service for similar molecular surfaces, eF-seek; (iv) identification of sequence and structural neighbors; (v) a graphical user interface to all known protein folds with links to the above applications, Protein Globe. Recent examples are shown that highlight the utility of these tools in recognizing remote homologies between pairs of protein structures and in assigning putative biochemical functions to newly determined targets from structural genomics projects.

for more

Tuesday, April 22, 2008

Dabur Sells Anticancer Business

Indian company Dabur India has sold its pharmaceutical division to German healthcare firm Fresenius Kabi. The asset mainly sells generic anticancer agents, and the purchase price was INR872 crore (US$219mn). BMI believes Dabur's real motivation behind the transaction was to focus on its core competency of fast-moving consumer goods (FMCGs), rather than the official line. According to Dabur's founder and director, Anand Burman, Fresenius is much better equipped in terms of international marketing capabilities to realise the full potential of the division. By not selling, Dabur would have being doing a 'disservice to the shareholders', he added.

Free UCSC Genome Browser Training

OpenHelix is providing free UCSC Genome Browser training for Institutions. You can apply for this at http://www.openhelix.com/seminars .


"The three and half hour introductory tutorial will cover the topics needed to effectively use this powerful, free, publicly-accessible tool, including: basic functionality of Genome Browser searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter. Participants will receive slide hand-outs, exercises, and a UCSC Genome Browser and Table Browser Quick Reference Cards."

Tribolium Genome Sequencing Consortium has released the Tribolium castaneum genome

Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell–cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development.

More at:
http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature06784.html http://www.bcm.edu/news/item.cfm?newsID=1090 http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&Cmd=Retrieve&list_uids=15718 http://www।hgsc.bcm.tmc.edu/projects/tribolium/


Monday, April 21, 2008

New York State Warns Consumer Genomics Services Firms about Offering Tests

The New York State Department of Health has sent warning letters to 23 firms involved in offering consumer genomics services and genetic tests to consumers, telling them that they need a permit to offer such tests and services. Among the firms that were sent letters were Navigenics, 23andMe, Affymetrix, Illumina, and HairDx. Iceland's DeCode Genetics, which offers a consumer genomics service and has been offering the test to New York state residents.

for more

Friday, April 18, 2008

Roughly 80 percent of known protein coding genes in Saccharomyces cerevisiae are nonessential

Using chemical genomics, researchers from Stanford University and the University of Toronto demonstrated that the majority of yeast nonessential single deletions exhibit growth defects when exposed to certain chemical or environmental stress. They also identified new candidate multi-drug resistance genes and demonstrated how clustering genes based on their co-fitness can provide clues about their function. The work appeared online today in Science.

“The emergent field of chemical genomics promises that, by understanding the relations between small molecules and genes on a systems level, we might understand genomic responses to small molecule perturbants,”

Do you want to know more?

see also

Gene Therapy CMC Guidance Released

The US Food and Drug Administration issued a final guidance last week regarding investigational new drug applications for human gene therapy. Although gene therapy is still in the developmental stages, there is much hope for gene-based treatment and products. Because the therapy involves replacing a patient's faulty genetic material with normal genetic material,there is concern about safety in making sure replacement cells continue to function as they should. The guidance, therefore, focuses on the type of information that scientists need to consider and include in their documentation when studying these drugs and submitting them for FDA approval.

Based on a draft guidance that was issued in November 2004 (69 FR 64958), the final document, Content and Review of Chemistry, Manufacturing, and Control (CMC) Information for Human Gene Therapy Investigational New Drug Applications (INDs), provides information on what to include in an original IND. The document also applies to combination products that contain a human gene therapy biological product in combination with a drug or device as part of the final product.

The full guidance is available for review and comment here.

Complete Darwin Papers Debut on Internet

Darwin's private papers online - the largest publication of Darwin's papers in history. Read about it here. Browse the papers here.

The complete works of Charles Darwin -- a god among scientists and the bane of every creationist’s existence – are finally available for anyone, anywhere to read. And it only took 126 years and another scientific revolution to make it happen.

Cambridge University, where Darwin studied theology, has digitized and published on the internet its collection of some 30,000 items and 90,000 images by the man who changed the course of science by writing the evolutionary primer, The Origin of Species, in 1859.

Cambridge was given the collection by the Darwin family and Pilgrim Trust after World War II. As described in 1960:

They were in parcels each containing small packets of manuscript wrapped in tissue paper on which the subjects had been noted in Darwin's hand. They were presumably just as Darwin left them, and accordingly this arrangement was preserved when they were bound, the volumes now representing as closely as possible Charles Darwin's papers in the order in which he left them. Beside the original papers there were copies of a large number of letters to Darwin, collections of press-cuttings, etc.

for more...


A centralized database of Indian Drug Commission approved drugs

Indian Drug Database
An attempt is made to collect/design the Indian approved drugs and the experimentally determined and computed three-dimensional (3D)-structures and their functional annotations are deposited...
Do you want to know more?

Nicholas Piramal India Limited to Piramal Healthcare Limited

Nicholas Piramal India Limited ("NPIL", name proposed to be changed to Piramal Healthcare Limited) is one of India's largest pharmaceutical companies, with a growth track record of above 30% CAGR since 1988. NPIL had consolidated revenues of US$602 million in 2006-07. The Company is currently ranked 4th in the Indian market with a diverse product portfolio spanning nine therapeutic areas. The Company is also one of the largest custom manufacturing companies with a global footprint of assets across North America, Europe and Asia. NPIL is listed in India on the National Stock Exchange (Ticker: NICOLASPIR) and the Bombay Stock Exchange (Ticker: 500302). The name change from Nicholas Piramal India Limited to Piramal Healthcare Limited is subject to approval by the Company's shareholders and Central Government.

Thursday, April 17, 2008

Version control system ideal for the collaborative bioinformatics software development

The new hotness, fast, efficient, distributed version control system ideal for the collaborative development of software...

Github, a source code management (SCM) repository based on git has exited beta and is ready for people to sign up. Git and github offer interesting opportunities for bioinformatics software development, and I think it’s worth taking a few minutes to explore them. There’s a free option too, so it doesn’t cost anything to sign up and play around.

Github builds on git and takes the easy branching feature a step further to create a social software site. I know everyone and their dog is creating a social [insert verb]ing application/site, but you might find that that github’s approach can make a difference in your approach to software development. Github makes it possible to see who is creating branches of your project, visualised as a network, where branch and merge points are shown in a timeline.

More on git and github

Repository Formats Matter

Moving from subversion to git

Video tutorial on using git

Comments in github

Project forking using github

Ruby on Rails moves to github

For Details: git, github, and bioinformatics software development


MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences

The Molecular Evolutionary Genetics Analysis (MEGA) software is a desktop application designed for comparative analysis of homologous gene sequences either from multigene families or from different species with a special emphasis on inferring evolutionary relationships and patterns of DNA and protein evolution. In addition to the tools for statistical analysis of data, MEGA provides many convenient facilities for the assembly of sequence data sets from files or web-based repositories, and it includes tools for visual presentation of the results obtained in the form of interactive phylogenetic trees and evolutionary distance matrices. Here we discuss the motivation, design principles and priorities that have shaped the development of MEGA. We also discuss how MEGA might evolve in the future to assist researchers in their growing need to analyze large data set using new computational methods.

Chennai is finally catching up in the Life Sciences & Informatics Race

Chennai is fast catching up lots of activity in the last 6 months in the field of Life Sciences and Informatics.

  1. HCL lifescience is now started operation form chennai in addition to their unit in Delhi
  2. A very ambitious venture spearheaded by none other than Dr. K.B. Chandrasekhar is Svapas
  3. TICEL biopark also has a few (Huclin Research, Histogenetics) but just CROs and others yet to have core informatics companies
  4. The early bird and one company which has been fighting and surviving all the odds Brain Waves has recently been creating vibes in the literature informatics and literature mining
  5. Neozene Bio Sciences has an office in chennai
  6. Vasta Biotech guess is a biotechnology firm
  7. Here a big wig GVK though is just testing the chennai waters with its biocampus
GVK Bio-has launched its new branch of bioCampus in Chennai Informatics division offering "Protein modeling and Drug Design"-training with recruitment program and projects for final year M.Sc, B.Tech, M.Tech, B.Pham, M.Pham students.

bioCampus
GVK Biosciences Private Limited,
#37, Sterling Road, Nungambakkam,
Chennai-600034
, India
T +91 044 - 66293000, 66293007
F +91 44 66293199
Mail to biocampus.chennai@gvkbio.com
Web: www.bio-campus.com

Wednesday, April 16, 2008

Position open dbSNP Curator

The Single Nucleotide Polymorphisms database (dbSNP) serves as a central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Computercraft seeks a biologist with significant knowledge in life sciences to help curate dbSNP records, process submission, and perform data analyst tasks. Candidates should also have the ability to rapidly develop applications to process data into database and to generate reports.

The individual will work onsite at the National Institutes of Health (NIH) in Bethesda, MD. Our scientists work with genomic experts at NIH's National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM) to create and enhance a suite of databases and tools available to researchers worldwide.

Requirements:
• PhD or M.S. in molecular biology, bioinformatics, or highly related field
• Linux/UNIX experience
• Relational database and SQL experience
• Programming experience (Perl, Python, or C++)
• Excellent verbal and written communication skills as well as organizational skills are essential
• Ability to work with a team in a production environment and communicate well with NCBI biologists and programmers as well as external scientist
• Strong interest in contributing to the development of public database resources
• Ideal candidate will have experience with dbSNP, genotyping, and QC processing

Other Desirable Experience:
• XML/XSLT
• Javascript and AJAX
• Web development

Additional information about the Single Nucleotide Polymorphisms is available at: http://www.ncbi.nlm.nih.gov/projects/SNP/


To apply for this position or learn about other Computercraft job opportunities, please visit the Careers section of our website: http://www.computercraft-usa.com/

Tuesday, April 15, 2008

Detecting non-coding sequences under functional selection is important to decode the genome

Genetic signals that govern gene splicing are under selective evolutionary pressure and are not the product of neutral evolution, new research suggests. The research, which appeared online this week in the Proceedings of the National Academy of Sciences, underscores the functional importance of splicing regulators। It also demonstrates a method by which exons and introns are differentiated in the genome.

see also

Monday, April 14, 2008

Café Scientifique

It is a chilly Tuesday night and outside the Dana Cafe in London a queue of young people spills on to the pavement. A glamorous woman with a walkie-talkie and clipboard guards the bar's door and turns away anyone who is not on the guest list.

The attraction is not the latest band, exclusive club or film screening, but a science lecture। Inside, Aubrey de Grey, a scientist from the Methuselah Foundation, a research group, is swigging from a bottle of Guinness as he tries to persuade a sceptical audience - which includes designers, artists and television producers - how society would benefit if we all lived forever.

Clutching a glass of red wine, Alex Wilkie, a 32-year-old design lecturer, believes that science is undergoing a revolution and should not be dismissed as nerdy. 'It's an increasingly scientific society that we live in,' he said. 'Understanding what's going on in science helps put everything in context.'

De Grey gives more than 30 such talks a year and believes that people are excited by the humanitarian potential of science, rather than the theory. 'By and large, young people are more open-minded about my message, but I wouldn't say that implies they're more interested in science,' he said. 'I think for most the interest is in the "why" first and the "how" second.'

Most science cafes are loosely affiliated through an international umbrella organisation called Café Scientifique, which was founded in Leeds in 1998 and inspired by the French Café Philosophique movement. There are now more than 30 across the country.

In a rare reversal of cultural exchange, it is one trend that Britain has exported to America, which is now home to 60 cafes. There are a further 120 worldwide. Founder Duncan Dallas said that by taking science out of the classroom it changed the expectation of both audience and speaker. 'Science is the most important force in our culture and is increasingly impinging on our public and personal lives, through subjects like genetics and climate change. So public engagement with science is bound to increase,' said Dallas. 'But, for me, the whole point of science cafes isn't to promote science or make more kids become scientists, but is about everyone being able to discuss topics which are revolutionary.'

The subjects discussed are diverse। One night at the Dana Cafe, in South Kensington, a hot debate raged about robotics, specifically a man-made fly-eating machine going by the name of 'EcoBot', which was invented by the Bristol Robotics Laboratory. Other topics include the smell of romance, the science of sleep and marine pollution.

for more details

Thursday, April 10, 2008

Microsoft Health & Life Sciences Developer and Solutions Conference 2008

Developers, architects, technical and business decision makers in the healthcare industry. Join to discover how Microsoft, its partners, and customers make possible the delivery of Software + Services in Health & Life Sciences.

April 22-24, 2008 Sheraton Hotel, Atlantic City, NJ
You may see the session details here and the registration details here.

"Modern bio-science is incredibly interdisciplinary now," Thanks-The life sciences are thriving

There was a time when bio-science was the Cinderella science: meticulous, certainly, and worthwhile, but far from glamorous. All that changed in 2003, when the sequencing of the human genome was completed.

Now masses of data and the potential for radical technologies are attracting the best graduates in chemistry, physics, engineering and maths. And bio-science offers more than intellectual curiosity, explains Professor Sir David Read, Biological Secretary and Vice-President of the Royal Society. "It's the human factor," he says. "Cross-disciplinary approaches are addressing many of the major threats to humanity: disease prevalence, antibiotic-resistant micro-organisms, avian flu, the threats to the environment associated with climate change."

The biological sciences are as varied, and sometimes as confusing, as life itself, taking in such disparate disciplines as neuroscience and taxonomy, environmental science and microbiology, physiology and biochemistry. At Cambridge University alone, there are 21 life-science departments.

What is exciting many dons at the moment is omics, or systems biology, which is allowing study to shift from single genes or proteins to how they work together in biological systems.

"The omics system is producing massive amounts of data that we have trouble finding people to make sense of," says Dr David Sargan, director of graduate education in the life sciences at Cambridge.

Mathematicians, physicists, chemists and engineers are all being brought in. "Modern bio-science is incredibly interdisciplinary now," says Professor Paul Freemont, head of molecular bio-sciences at Imperial College London.

Systems biologists are building mathematical models that simulate the living cell, synthetic biologists are redesigning biological systems, chemical biologists are probing living systems at the chemical level, and physicists and engineers are bringing imaging wizardry to bear in biology, from the molecular to the cellular level.

"The biological sciences are going through a revolution," says Professor Freemont. "It's very exciting in the life sciences right now. Students from other disciplines find it fascinating: they see this wonderful opportunity to develop new strands of science."

Interesting: Do you want to know more?



Biotech chief shifts investment focus

“We are changing the Merlin brand to reflect the move from early-stage biotechnology and our interest in the later stages of research,” Sir Christopher said.

The biotechnology sector was dealt another blow on Wednesday after Sir Christopher Evans, the biotechnology entrepreneur caught up in the cash-for-honours investigation, said he was starting a new investment firm that would not fund early-stage biotech companies.

Merlin Biosciences, the name of Sir Christopher’s venture capital firm known for providing much-needed seed funding to the industry, is being scrapped and its three funds are being transferred to a new company called Excalibur, which will provide services from venture capital to corporate finance and private equity.

for more details

Drug Alerts Sent Instantly to U.S. Doctors via Email

Welcome to the Health Care Notification Network (HCNN), the only secure online service that delivers urgent patient safety alerts to healthcare providers.

A new network to deliver drug safety alerts online to U.S. physicians was launched today, replacing a widely criticized and decades-old system based upon paper and U.S. mail. The Health Care Notification Network ("HCNN") is the result of a three-year effort and an unprecedented collaboration between U.S. medical society leaders, liability carriers, health plans, consumer advocacy groups, government leaders and industry, including major pharmaceutical manufacturers. The HCNN will also be available for rapid communication with physicians in the event of emergency public health or bio-terror events.

for more details

Videos about Science, Visualization, Research and more

Videos in Biosciences

Semi-automated workflows - Taverna Interaction Service

Have you been wondering about possibility of automating every scientific workflow? :

The Taverna Interaction Service: enabling manual interaction in workflows by Anders Lanzén and Tom Oinn

Taverna is an application that eases the integration of tools and databases for life science research by the construction of workflows. The Taverna Interaction Service extends the functionality of Taverna by defining human interaction within a workflow and acting as a mediation layer between the automated workflow engine and one or more users.

Try Taverna plugin is very likely an answer to automation of bioinformatics workflows...
(Bioinformatics Advance Access abstract)

Wednesday, April 9, 2008

Protein data bank archives 50,000th molecule structure

Research archive doubles in size since 2004

NEW BRUNSWICK, N.J. The Protein Data Bank (PDB) based at Rutgers, The State University of New Jersey, and the University of California-San Diego (UCSD) this month reached a significant milestone in its 37-year history. The 50,000th molecule structure was released into its archive, joining other structures vital to pharmacology, bioinformatics and education.

With its origins in a handwritten petition circulated at a scientific meeting, the PDB is the single worldwide repository for the three-dimensional structures of large molecules and nucleic acids। This freely available online library allows biological researchers and students to study, store and share molecular information on a global scale.

Officially founded in 1971 with seven structures at Brookhaven National Laboratory, the archive is managed by a consortium called the worldwide Protein Data Bank (wwPDB).

Today, the PDB archive receives approximately 25 new experimentally determined structures from scientists each day and more than 5 million files are downloaded from the PDB archive every month. Users include structural biologists, computational biologists, biochemists, and molecular biologists in academia, government and industry as well as educators and students.
Notable examples include recent structures of the adrenergic receptor, which will revolutionize the discovery of drugs to fight heart disease, allergies and numerous other diseases, and the structures of many enzymes from HIV, which have been pivotal in the design of new therapies to fight AIDS.

Advances in science and technology have helped the archive grow by leaps and bounds in the last 10 years, said Helen M। Berman, director of the RCSB PDB and Rutgers Board of Governors professor of chemistry and chemical biology, noting that the size of the PDB has doubled in just the last three and a half years.

We are estimating that the PDB will not only double but triple to 150,000 structures by 2014, said Philip E. Bourne, associate director of the RCSB PDB and professor of pharmacology at the UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences.

for details visit:

Protein data bank archives 50,000th molecule structure

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Tuesday, April 8, 2008

GenBank celebrates 25 years of service

Leading scientists discuss DNA database at April 7-8 Meeting

For a quarter century, GenBank has helped advance scientific discovery worldwide. Established by the National Institutes of Health (NIH) in 1982, the database of nucleic acid sequences is one of the key tools that scientists use to conduct biomedical and biologic research. Since its creation, GenBank has grown at an exponential rate, doubling in size every 18 months. In celebration of this vital resource and its contribution to science over the last 25 years, the National Center for Biotechnology Information, National Library of Medicine (NLM), NIH, is holding a two-day conference on GenBank.

The conference will take place April 7-8, 2008 at the Natcher Conference Center on the main NIH campus in Bethesda, Maryland. For details on the meeting, see the conference Web site, at http://www.tech-res.com/GenBank25. The conference is open to the public and also will be available via live and archived webcast; the April 7 proceedings can be viewed at http://www.videocast.nih.gov/summary.asp?live=6670 and the April 8 proceedings at http://www.videocast.nih.gov/summary.asp?live=6671.

The conference will bring together a slate of world-renowned scientists in molecular biology, genetics, bioinformatics and other areas to discuss GenBank's applications, the discoveries it has enabled, its history, and future directions. Speakers include Rich Roberts, Ph.D., a Nobel Prize winner for his discoveries of split genes, and currently Chief Scientific Officer at New England BioLabs; Sydney Brenner, Ph.D., a Nobel Prize winner for his work on genetic regulation of organ development and programmed cell death, and currently a professor at the Salk Institute; Francis Collins, M.D., Ph.D., who led the Human Genome Project and is Director of NIH's National Human Genome Research Institute; and Craig Venter, Ph.D., who led the private-sector effort to sequence the human genome and is President of the J. Craig Venter Institute. More than a dozen other eminent scientists will be speaking; the full list of presenters can be viewed at the GenBank conference Web site.

"Each day, researchers across the world submit tens of thousands of sequences to GenBank and collaborating databases in Europe and Japan," said Donald A. B. Lindberg, M.D., Director of the National Library of Medicine. "Because of these contributions, GenBank has become an essential tool for molecular biology. The National Library of Medicine is proud to partner with the research community in making this valuable resource available."

Rich Roberts, Ph।D., Chief Scientific Officer at New England BioLabs, commented, "GenBank has provided a foundation upon which much of contemporary biology is now based. It is becoming almost impossible to conceive of any serious biological study of a new organism that does not begin with the determination of its DNA sequence, which of course must be stored in GenBank." Roberts, one of the early proponents of the database, added, "the availability of this wealth of sequence information in a single repository is something we could only dream about in 1979 at the Rockefeller Conference that led to its creation and which we could not imagine being without today."

for more details



Friday, April 4, 2008

Productivity tools-Simulation Software Selected as Application of Choice by Premier Pharmaceutical Company

A leading provider of software for pharmaceutical discovery and development, today announced that the pharmacokinetics, dynamics, and metabolism science board at a top three pharmaceutical company named its software an "application of choice."

As pharmaceutical companies face a significant number of patent expirations in the near future, there is a need to become more aggressive in research and development to fill the pipeline, sometimes with reduced R&D staff.

Productivity tools in the field of pharmacokinectics, ADMET, chemical data visualization and analysis, etc. that leverage the expertise of the industry's scientific teams. It is believed that the difficulties facing some parts of the pharmaceutical industry will result in greater use of such tools as managers realize that the savings in time and money that can be achieved through their application vastly exceeds the cost of obtaining and learning to use them.

British researchers create human-animal hybrid embryo amid political row

For the first time in Britain, researchers at Newcastle University said Tuesday they had created human-animal hybrid embryos, amid a political row over a disputed embryo research bill in parliament.

According to the northern English university, the research, which was first presented at a lecture in Tel Aviv on March 25, has yet to be published or verified, with a spokesman for the university telling AFP that the institution "wouldn't claim it to be final at all."

The revelation comes with British MPs engaged in a fierce battle over the Human Fertilisation and Embryology Bill, which allows the creation of human-animal hybrid embryos for medical research.

Prime Minister Gordon Brown's governing Labour Party conceded in March that its party lawmakers with moral or ethical objections would be allowed to vote against parts of the proposed legislation when it comes before parliament this year.

The embryos were created by injecting DNA taken from human skin cells into eggs derived from cow ovaries with almost all their genetic material stripped away, and lasted for three days in a laboratory.

The Newcastle University spokesman said that the research would likely be published in "months rather than weeks".

At present, researchers wanting to create such embryos have to apply for a license from the Human Fertilisation and Embryology Authority, which currently regulates the practice in Britain, and hybrid embryos have to be destroyed after 14 days.

The government says that the scientific advantages of allowing the creation of hybrid embryos for research purposes could help millions of people to recover from illness or disease.

Religious leaders, however, have argued against the bill, with the leader of Catholics in Scotland, Cardinal Keith O'Brien, using his Easter Sunday sermon to brand the bill a "monstrous attack on human rights, human dignity and human life" which will allow experiments of "Frankenstein proportion".

for more info and images visit

Tuesday, April 1, 2008

All for the love of code...

Google Summer of Code™


Google Summer of Code 2008 is on! Over the past three years, the program has brought together over 1500 students and 2000 mentors from 90 countries worldwide, all for the love of code.

http://code.google.com/soc/2008/

GENSEQ is recruiting Bioinformatics Programmers and Software Developers

Genseq Ltd., is a Jersey-based privately-held personal health and genomics company.

We are currently recruiting Bioinformatics Programmers and Software Developers to work in our Cyberjaya, Malaysia office.
Please find the job descriptions and requirements at www.123genes.com/jobs . If you are interested, apply online Or submit your CV with a cover letter highlighting relevant experience to hr@genseq.co.uk on or before 10th April 2008.
Shortlisted candidates will be called for the recruitment test later in April, 2008 at Hyderabad, India. (If you have already applied, you do not need to reapply)

If you cannot find a specific position that fits your skill set, you may send your CV and Cover letter to hr@genseq.co.uk

Benefits
Benefits include generous salary, medical, dental, participation in staff bonus pool, monthly travel allowance, complimentary beverages and an annual company trip. Being located in our Malaysia Bioinformatics Office, you will also be in one of the most interesting countries in South Asia - a fusion of Malay, Chinese, Indian and indigenous cultures.

CAS numbers are not public domain, are they?

"Work created before the existence of copyright and patent laws also form part of the public domain. The Bible and the inventions of Archimedes are in the public domain. However, copyright may exist in translations or new formulations of this work." [Wikipedia]
As posted by Tony is the Chemical Abstract Service (CAS) discouraging using their CAS services for assigning correct CAS numbers to structures for any third party database. Wikipedia is a source of structures, which is public domain due to its GNU FDL. Still, this does not imply that any translation of structures, e.g. CAS numbers, are in the public domain, too. Honestly, this raises a serious problem for curating CAS numbers on Wikipedia and this raises indeed the question, if they should not be dropped from Wikipedia, and any other information source, at all? Is it not better having no information, than having wrong information?

A CAS number is for me only one certain translation of a chemical structure. In this case, the only source and creator for CAS numbers is the American Chemical Society. CAS claims that their services can not be used for curating other data sources. Does this also mean that people can not use CAS numbers from publications?
"The public domain can also be defined in contrast to trademarks. Names, logos, and other identifying marks used in commerce can be restricted as proprietary trademarks for a single business to use. Trademarks can be maintained indefinitely, but they can also lapse through disuse, negligence, or widespread misuse, and enter the public domain. It is possible, however, for a lapsed trademark to become proprietary again, leaving the public domain." [Wikipedia]
And does this also mean that scientists are basically not allowed publishing CAS numbers and structures in scientific publications? How can CAS numbers then be used at all, if we can not store this information?

Many questions, and who will answer them? And, if they got answered what is the way forward for getting curated structures within the public domain? I would say (again, this time in nicer words): 'get organized scientists worldwide!' If CAS can do it, we can do it? It may take longer to get the party started, but if we do not start it will never happen.
"An ideal collaborative resource would be designed for large-scale data mining, contain curated historical data, and have data standards and deposition tools that could constantly bring in data from the published literature. ... In other words, the party might take longer to get started than hoped for, but it should be worth the wait." [M. Baker, DOI 10.1038/nrd2148]

Source: CAS numbers are not public domain, are they?

Life Science and Informatics

What is this?
is this a new industry?
or a old wine in a new bottle?

Well Life Sciences and Informatics can be anything form computational biology, all omes and omics, core bioinformatics to curation and literature mining, database creation, in the area of biology, chemistry , bio-chem space.

There are number of companies in India and bangalore is the forefront as a major bio-cluster with 20 to 30 companies in this sphere.

now how good are these companies doing?
how good are they in terms of the international markets and how profitable is their business?
what do they do?
their clients?

These are some interesting things that could be discussed in this blog page...

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