Science and Genetics -The Hollywood Connection

 

I thought of actually righting about presence of genetics genomics and biology in Hollywood and popular entertainment and books, here is a collection of blogs and websites on the topic

Prestigious journal makes science sexy again- Scientific American

Science of TV impure but CoolExpert Voice Tv science

Best science fiction Movies – Gadget Maniac

Hollywood on HereditoryThe scientist  

Genetics in BigscreenScience Fiction Biology

Genetics in Movies – GxP genetics Expression

Super Heroes  Watch Mojo

Genetics and culture – Wagner Institute

Genetics Silver screen –USATODAY

Holyywodd frightend of genetics- End of Universe

Genetics art and culture –Centre for Genomics and Society

How Hollywood Vilifies A People –Daily Sun

THE GENOMICS MOVIES

The Island of Dr. Moreau
http://www.imdb.com/title/tt0116654/

Reversing Darwin’s Theory
http://www.imdb.com/title/tt0241382
Murders in the Rue Morgue
http://www.imdb.com/title/tt0023249

28 Days Later
http://www.imdb.com/title/tt0289043/   

She Demons
http://www.imdb.com/title/tt0052187/

Wolf
http://www.imdb.com/title/tt0111742/

JK Jackson, “Mothering the monsters,” The Scientist, September 1, 2006.
http://www.the-scientist.com/news/display/24578/

Hulk
http://www.imdb.com/title/tt0286716     

Life Without Soul
http://www.imdb.com/title/tt0005615/                                       

Spider-Man
http://www.imdb.com/title/tt0145487/ 

Humunculus
http://www.imdb.com/title/tt0006820    

GATTACA
http://www.imdb.com/title/tt0119177

 

next generation literature awareness tool

Another science website that seems to be as taking its cues from web2.0 anthology.

Faculty of 1000 Biology is the next generation literature awareness tool. It is a revolutionary new online research service that will comprehensively and systematically highlight and review the most interesting papers published in the biological sciences, based on the recommendations of a faculty of well over 1000 selected leading researchers.

Faculty of 1000 Biology will be run by scientists for scientists, and will provide a rapidly updated consensus map of the important papers and trends across biology.

In the Faculty of 1000 Biology, the entire field of biology is divided into 16 Faculties (subjects), each of which will be run by two to four Heads of Faculty.

Each Faculty is subdivided into 3-12 Sections, each run by two or three Section Heads and comprising between 10 and 50 Faculty Members. Faculty of 1000 Biology aims to invite the best scientists internationally in each field and to involve both experienced and younger investigators.

All in all an excellent website with lots of information which is peer reviewed

microarray for transgenomics studies and Study of Evolution of organisms

Barcode microarrayshas demosntrated the various ways in which the microarrays can be used in various ways.Though mirred in controvesy as any new technology has been subjected in its infancy, the basic principles behind the technology can be put to use in many other frontiers. It may be optimized to study transgenomics organims and its evolution. To study the development of drug resistance bacteria and virus. To find out how microbes evolve though all this may require new approaches it all could stem from the basic principles adopted by DNA microarry and barcode microarray and SNP arrays

Consolidation in Oligo industry and Growth for India based companies and outsourcing value proposition in Genomics and microarray/oligo industry

Ocimum Biosolutions acquires European based Oligo manufacturing company – Isogen Life Science

November 17, 2006, IJsselstein/Hyderabad – Ocimum Biosolutions, a leading provider of laboratory information management systems (LIMS), bioinformatics solutions, Microarrays and contract research headquartered in Hyderabad, India, has acquired the BioMolecules synthesis business of Isogen Life Science based in The Netherlands.

Ms. Anuradha Acharya, CEO of Ocimum Biosolutions said “We are very pleased to have taken a significant step towards becoming a global oligo player with the Isogen acquisition. We will continue looking for targets in related areas to scale up our oligo production capability. This acquisition will also help us become a more integrated genomics services provider with three delivery points in Indianapolis, IJsselstein and Hyderabad.”

Mr. Hans Beijersbergen van Henegouwen, MD of Isogen Life Science said, “It is an excellent opportunity for the Biomolecules Division of Isogen Life Science to become a global player in this competitive business. The new business configuration will be much more flexible and will be able to play an important role in the vast growing demand for oligo nucleotides all over the world. Ocimum is the perfect partner for fulfilling a broad platform of needs in this market segment.”

Avendus Advisors was the sole financial advisor to Ocimum for the deal. Commenting on the transaction, Shiraz Bugwadia, A.V.P., Avendus Advisors “Ocimum is one of the few Indian players within the BioIT and microarrays space to have scaled up successfully over the last couple of years. Ocimum has also been successful at using the inorganic route to scale rapidly by acquiring niche good quality companies in Europe such as MWG Biotech’s division and now Isogen Life Science.”

About Isogen Life Science:

Isogen Life Science (www.isogen-lifescience.com) is a leading supplier of products for the life science sector. The company provides a wide range of instruments, reagents and consumables in the areas of cell biology, molecular biology and biochemistry.

Isogen Life Science is a merger between B&L Systems (1987), the Benelux distributor for scientific instrument companies, and Isogen Bioscience (1988), a leading producer of DNA, RNA, peptides and related products, which are used around the world by pharmaceutical and biotechnology companies and leading research institutes.

About Ocimum Biosolutions:

Ocimum Biosolutions is a life sciences R&D enabling company with three main focus areas, BioIT, Microarrays and Contract research services. The US operations of the Company focuses on custom contract research services in the molecular biology area while the Indian operations provide BioIT services and Microarrays. Ocimum has more than 300 prestigious clients worldwide including the Centres for Disease Control, University of Toronto HIV clinic, National Research Council of Canada, Dow AgroSciences, Max Planck Institute etc.

Ocimum has adopted an inorganic strategy to ramp up the business fast and has demonstrated its capability to execute this strategy in the past. As a part of its strategy, Ocimum acquired a division of MWG Biotech, Germany in 2005. The Company has received a host of awards and recognitions. The Company has recently received the IT Innovation award by NASSCOM, presented by H.E. the President of India. Also, Red Herring magazine picked Ocimum as one of the eight compani es to watch in India. Deloitte ranked the Company as 4th Fastest growing Technology company in India and the Fastest growing Life Sciences Company in India.

For more information, please visit: www.ocimumbio.com

Indian company gets 6.5 million USD IFC funding to promote contract research in bioinformatics and genetics industry

Hyderabad, November 15, 2006 – Ocimum Biosolutions today announced that International Finance Corporation (IFC), the private sector arm of the World Bank Group, will invest USD 6.5 million of equity, for a minority stake, and debt in the Company. Funds raised from this transaction will be used for financing both organic as well as inorganic growth of the Company.

Says Ms. Anuradha Acharya, Founder & CEO of Ocimum Biosolutions, “We are very happy to have IFC as our partner for growth. These are exciting times for Ocimum and to have IFC as an investor in the company brings a lot of confidence in our clients and partners.”

Iyad Malas, IFC’s Director for South Asia, said, “IFC’s support to Ocimum will provide the company its much needed growth capital to establish an internationally competitive contract research outsourcing company and promote the discovery of new drugs at lower costs. We will also help institute improved corporate governance standards.”

This is Ocimum’s first round of fund raising from private equity investors. The Company is contemplating another round of fund raising in the next 18-24 months.

Recently, Ocimum acquired a Europe based oligo manufacturer. The Company is also scouting for more targets in the European market.

Avendus Advisors was the sole financial advisor to Ocimum for the deal. Commenting on the transaction, Shiraz Bugwadia, A.V.P., Avendus Advisors “Ocimum is one of the few Indian players within the BioIT and micro arrays space to have scaled up successfully over the last couple of years. Ocimum has also been successful at using the inorganic route to scale rapidly by acquiring niche good quality companies in Europe such as MWG Biotech’s division and now a Netherlands based oligos manufacturer.”

About Ocimum Biosolutions:

Ocimum Biosolutions is a life sciences R&D enabling company with three main focus areas, BioIT, Microarrays and Contract research services. The US operations of the Company focuses on custom contract research services in the molecular biology area while the Indian operations provide BioIT services and leverage on India’s low cost advantage in IT space. The Company enjoys a strong brand image in the market and has worked with some of the best research organizations in the world like IIT Kharagpur, National Research Council of Canada, Agriculture and Agri Foods, NIH, Dow Agro Sciences, etc.

Ocimum has adopted an inorganic strategy to ramp up the business fast and has demonstrated its capability to execute this strategy in the past. As a part of its strategy, Ocimum acquired a division of MWG Biotech, Germany in 2005. The Company has received a host of awards and recognitions. The Company has recently received the IT Innovation award by NASSCOM, presented by H.E. the President of India. Also, Red Herring magazine picked Ocimum as one of the eight companies to watch in India and was a winner of Red Herring’s Asia 100. Deloitte ranked the Company as Fastest growing life sciences company in India.

For more information, please visit: www.ocimumbio.com.

About International Finance Corporation:

The International Finance Corporation, the private sector arm of the World Bank Group, is the largest multilateral provider of financing for private enterprise in developing countries. IFC finances private sector investments, mobilizes capital in international financial markets, facilitates trade, helps clients improve social and environmental sustainability, and provides technical assistance and advice to businesses and governments. From its founding in 1956 through FY06, IFC has committed more than $56 billion of its own funds for private sector investments in the developing world and mobilized an additional $25 billion in syndications for 3,531 companies in 140 developing countries. With the support of funding from donors, it has also provided more than $1 billion in technical assistance and advisory services.

For more information, please visit www.ifc.org.

can open source ideals begin to give a real answer to biotech’s future

would it be possible to adopt the ideals of the open source in microarray development, there has been many research works that can be hailed as open source ideals in the biotechnology space, human genome project can be the perfect example, But apart from the few attempts by academia and non profits institutions there havnt been many attempts to look at this as a way forward, Microarray development can be termed as a lucrative field where such a coalition would accrue great benefits, By releasing the research works for others for free of cost it is possible to bring down the cost of microarray, there is no doubt that it would benefit the new research frontiers such as pharmacogenomics and toxicogenomics, by reducing the cost per array closer to any to other screening test currently adopted in hospitals or used by forensic labs. Microarray can also be used for reducing the costly PCR technique by closing in on a more focused number of genes to amplify from But it would mean that there has to be enough researchers out there who will be buying theses product in the first stage itself so as the company involved i such an audacious attempt would recover its cost and make profits to continue further work, thats a major hurdle to overcome, as custom microarray or at times even the existing one may not be useful to every researcher even if they are working on the same genome for example one person may be in toxicology research and the other in ecology or pure genetics even if they work on same genome the controls required and number of gene of interest would vary vastly across the spectrum, it may take a long time for the open source ideals to bear any fruit in this arena but that may be the way forward to bring meaningful results with less cost, till outsourcing can be a start for all things to come

 Abin paul Xavier

http://www.ocimumbio.com

microarray software

Ocimum Biosolutions is a life sciences R&D enabling company with three focus areas, BioIT, Microarrays and Research services. The Microarray division of Ocimum has been recently acquired from MWG Biotech. These include Catalog “OciChip”, Custom “OciChip” and microarray services.

Ocimum biosolutions offers an           Affymetrix compatable smicroarray software            microarray analysis software called Genowiz, An evaluation copy of the software is avaialble at http://www.coimumbio.com

Genowiz™

Genowiz™ is a powerful gene expression analysis program that has been designed to store, process and visualize gene expression data efficiently. It includes a suite of advanced analysis methods and allows researchers to select analysis methods appropriate for their dataset. Genowiz™ allows researchers to organize experimental information (MIAME), import data files quickly and easily, work with multiple experiments at the same time, import gene annotation files, pre-process and normalize data, perform cluster analysis, classify and view gene information, perform functional classification and track down intricate correlations in data by performing pathway analysis. All analysis done is tracked, saved into a database and can be retrieved at any point of time.

 


What’s New
• Import Affymetrix Raw Data
• Merge Clusters
• One Sample t-Test
SVM
View and Update NetAffx™ Annotations
• Annotation Views
• URL Editor
• Search for Gene Ontology and Pathway terms
• Regulatory, Signal Transduction and Disease Pathways

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Data and Gene List Import
Genowiz™ supports a wide range of data formats pertaining to cDNA and Affymetrix data. Users can directly import .CEL and .CDF files into Genowiz™. Users also have an option to upload data in customized formats. Customized uploader allows users to add and save new data formats. One-Click Uploader can then identify these formats.

Gene List files for annotating genes can also be imported.

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MIAME
Minimum Information About a Microarray Experiment (MIAME) facilitates adoption of standards for microarray experiment annotation and data representation. Genowiz™ focuses on establishing standard microarray experimental data repositories and information sharing within the scientific community. Researchers can also exchange MIAME data by using MAGE ML document exchange format.

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Data Transformation, Normalization and Filtration

In any type of expression analysis, pre-processing of data to reduce undesirable variation among datasets and to bring data to a common platform is a vital step. Genowiz™ provides users with a wide range of data transformation, normalization and filtration tools. These include:

Data transformation options such as imputation of missing values, log transformations, mean/median, Z-transformation, subtract control, divide by control, scaling etc.
Normalization techniques such as normalization for dye swap replicates, cDNA raw data normalization options (cDNA Loess and Print tip Loess) and quantile normalization. Separate normalization techniques are provided for cDNA and Affymetrix arrays. Normalization can be done using all genes or control genes.
Filter data based on replicate genes, fold change, mean, standard deviation, calls and missing values. Replicate samples are handled using various parametric/non-parametric tests. Multiple testing correction can be applied to reduce false positives.

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Data Analysis and Visualization
Genowiz™ comes equipped with several data analysis tools. Complete with excellent graphics, it is an excellent tool for interpretation of biologically meaningful results. Some of these tools include partition clustering, hierarchical clustering, SOM, PCA, gene shaving and discriminant PCA and SVM. Option for merging, clusters of interest has also been provided.

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• Partition Clustering (K-means, Forgy’s)
This tool classifies genes or samples in user-defined groups using distance parameters. The obtained clusters can be re-clustered. Re-clustering utility helps scientists pick a set of genes of their interest. A 2D PCA view shows the distribution of genes in various clusters.

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• Hierarchical Clustering
One of the most important tools for studying relations between genes, this tool creates a dendrogram based on the relative distance between genes. The different optional parameters help the user in correctly determining the relationship between two genes. Models of analysis include single linkage, complete linkage and average linkage clustering. Genes, samples, or both together can be clustered.

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• Self Organizing Maps
A two-way classification of genes into clusters based on novel artificial neural networks is an integral feature of data clustering tools in Genowiz™. This gives a deeper insight into clusters, as neighboring clusters are very similar to each other.

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• Principal Component Analysis
This tool involves a mathematical procedure that transforms a number of (possibly) correlated variables into a (smaller) number of uncorrelated variables called principal components. These provide an insight into existent variability in the data.

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• Gene Shaving
This method identifies subsets of genes with coherent expression patterns and large variation across conditions. Gene shaving differs from hierarchical clustering and other methods of gene expression analysis in that genes may belong to more than one cluster.

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Classification

Classification algorithms are used to classify samples, based on information from similar samples with known classes that are available in training data. In Genowiz™, Support Vector Machines (SVM) and Discriminant PCA are used to predict classes for unclassified samples.

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Biological Analysis
Genowiz™ annotates genes and classifies them into functional categories (Gene Ontology). Option of importing annotation files is also provided. Integrated pathways module aids researchers in understanding metabolic pathways in relation to expression data. Pathway maps edited/created can be associated with author details too. Coupled with biological information and gene ontological classification, it forms an excellent tool in understanding biological systems. Search can be performed on the gene ontology and pathway tree to look for ontologies or pathways of interest.

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Utilities

Several utility options are present to add value to the analysis performed:

Gene List Comparison: Subtle relations among datasets can be probed using this feature.

Pattern Simulation: An expression pattern can be defined and Genowiz™ lists out all genes with a similar expression pattern. This gene list can be saved and exported.

Gene Tracking: Important genes or genes of interest can be tagged and tracked throughout the analysis.

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View and Update NetAffx™ annotations

Annotations for the uploaded data can be viewed by connecting to NetAffx™ database. Connecting to the NetAffx™ database and selecting a corresponding chip will retrieve annotations from that chip. Flexibility to update annotation information for existing chips and add annotation information for new chips is also present, thus enabling researchers to view updated annotations for chips.

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Technical Support
Ocimum’s technical support staff is available 24 hours, five days a week, to answer your questions about Genowiz™ over phone, e-mail and web chat. All questions previously answered by the support staff are available on the website for visitors.

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