Cloud computing has gotten a lot of attention in the last couple of years.  As a result, countless companies (such as Amazon, Rackspace, etc) now offer services for those who need quick access to servers and storage- without the need for server rooms, full time sys admins, etc.

So with all of these pre-existing services for doing cloud computing, why are we creating our own?  There are a few reasons, but one important reason is that scientists often work with BIG data.  When a user needs to upload and/or download hundreds of gigabytes, or even terabytes of data from the cloud, they are limited by the network speeds between their computer and the cloud.  Within the university, we have very good network speeds, which makes it feasible to transfer large datasets to and from servers. What may take hours to transfer to the Amazon Cloud may take minutes to transfer to the Genome Center Cloud.

Service and expertise are another place we hope to add value to the cloud experience.  The Bioinformatics Core has a lot of experience installing and using various scientific software, which we can use to save users hours of frustration when trying to get their research going.  Other services are great, but their only aim is to provide computing resources.  The Bioinformatics Core is here to help you do science!

At the moment, most cloud computing services are aimed at more “run of the mill” users.  Bioinformaticians are a demanding bunch, and when they need a high memory (think 500GB or RAM) or powerful (imagine 50 cores) machine to do an analysis, commercial solutions fall well short (generally they don’t offer more than 70 GB of RAM or 8 cores).

We are currently working on building the necessary infrastructure, and are aiming to make the cloud available to customers by fall 2013.  If you are interested in using the Genome Center Cloud, please email us at ucdbio@gmail.com.

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Source:kenresearch

The report titled “India Bioinformatics Industry Outlook to FY’2018 - Surging Government Initiatives to Foster Future Prospects” provides a comprehensive analysis of the market size of the India bioinformatics industry by revenue from domestic sales and exports, market segmentation of bioinformatics by application in different sectors such as agriculture biotechnology, medical biotechnology, animal biotechnology, environmental biotechnology, forensic biotechnology and others, by products and services such as bioinformatics knowledge management tools, bioinformatics services and bioinformatics platforms and by various applications such as genomics and transcriptomics, proteomics and metabolomics, pharmacogenomics, molecular phylogenetics and drug design. The report also entails the market share of major bioinformatics companies in India by revenue along with the company profiles of major bioinformatics and genomics companies. An analysis of the future of India bioinformatics industry is provided on the basis of revenue of the market over next five years.

The bioinformatics sector in India has faced many challenges over the years; however this industry has managed to sustain itself and has showcased healthy growth.

The industry has grown at a CAGR of 12.3% over the period FY’2007-FY’2013 and reached INR ~ million in FY’2013. The rising trend in the growth rate of domestic revenue in the bioinformatics market in India has paced since FY’2010. In FY’2012, the domestic bioinformatics market generated revenue of INR ~ crores which constituted ~ % of the revenue of the bioinformatics market in India. During FY’2010-FY’2013, the revenue created by exports was on an average ~ % of the entire bioinformatics revenue in India. Public funding towards research and development (R&D) from the Government of India, decline in costs of human genome sequencing, increase in R&D investments by companies and increase in the number of orders for contract research activities are leading to the increase in bioinformatics revenue in India.

The use of bioinformatics in the agriculture biotechnology sector has grown at a CAGR of 13.9% over the period FY’2007-FY’2013. The contribution of medical biotechnology to the overall bioinformatics market in India has witnessed an increase from ~% in FY’2007 to ~% in FY’2013. In FY’2013, animal biotechnology contributed nearly ~% in the bioinformatics revenue whereas the contribution of environmental biotechnology was recorded as ~% during the year. Forensic biotechnology has grown at a CAGR of 6.1% during the period FY’2007-FY’2013 while marine biotechnology and academics generated revenue of INR ~ crores in FY’2013.

The products and services segment of the bioinformatics industry in India has been majorly driven by the bioinformatics services. The bioinformatics services have grown at a CAGR of 14.2% during FY’2007-FY’2013 and reached a revenue figure of INR ~ crores in FY’2013. The bioinformatics knowledge management tools generated a major part of the revenue from the sequence analysis tools over the years. In FY’2013, the revenue from the tools segment was INR ~ crores. Bioinformatics platforms generated revenue of INR ~ crores in FY’2013 which is considerably higher as compared to the revenue generation of INR ~ crores in FY’2007.

In FY’2013, genomics and transcriptomics held nearly ~ % of the overall bioinformatics market revenue in India followed by proteomics and metabolomics which accounted for ~ % of the overall revenue of the bioinformatics market in the country in FY’2013. The revenue generated through application of pharmacogenomics in bioinformatics market in the country was INR ~ cores. Pharmacogenomics segment grew at a CAGR of 12.4% during the period FY’2007-FY’2013. Molecular phylogenetics forms ~ % of the total bioinformatics revenue in FY’2013 while ~ % of the revenue was generated through the field of drug design for the overall bioinformatics sector in India.

The bioinformatics market in India is highly fragmented with a large number of mid-sized and small players. A few large players contribute a major part of the revenue of the industry. The bioinformatics market in India is largely held by Strand Life Sciences, Ocimum Biosolutions and Molecular Connections which captured nearly ~% of the market in FY’2013. Strand Life Sciences is the largest player in bioinformatics market in India, capturing a market share of ~ % in FY’2013. Companies from the information technology (IT) sector are also gradually gaining a foothold in the bioinformatics industry in the country, by developing innovative products and services.

The ongoing trends in the bioinformatics industry in India have showcased that genomics, translational bioinformatics and personalized medicine will be the major driving segments of the industry over the next few years.

Key Topics Covered in the Report:

1. The market size of the Indian Bioinformatics Industry , FY’2007-FY’2013
2. Market segmentation of India bioinformatics industry by application by sectors, FY’2007-FY’2013
3. Market Segmentation of India bioinformatics industry by products and services,FY’2007-FY’2013
4. Market Segmentation of India bioinformatics industry by applications of bioinformatics ,FY’2007-FY’2013
5. India bioinformatics industry trends and developments
6. Government regulations and initiatives of India bioinformatics industry
7. Major bioinformatics research institutes in India
8. Market Share of leading players in bioinformatics industry in India,FY’2013
9. Company profiles of major players in India bioinformatics industry
10. Future outlook and projections on the basis of revenue in India bioinformatics market, FY’2014-FY’2018

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Source: Techcrunch

Dr. Pollard will share her experience at the cutting edge of scientific research, as founder and faculty supervisor of the Gladstone Bioinformatics Core and an associate professor at the Institute for Human Genetics at the University of California, San Francisco. Pollard’s lab is known for developing statistical and computational methods that enable the analysis and study of massive genomic datasets. With her research focusing on genome evolution and the relationship between DNA sequences and biomedical traits, Pollard’s work has important implications for how science identifies and treats a wide range of diseases, from AIDS to atherosclerosis.

Together, Tecco, Douglas, Kaplan and Pollard will talk about how they are building their own businesses, what they’ve learned and how they plan to leverage the changes in technology to build a healthier world.

The conference starts September 7th and runs until the 11th at our favorite location, the San Francisco Design Concourse. Stay tuned for more speaker announcements and a few surprises to be announced soon.

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The Search for America's Next Top Young Scientist 

The 2013 Discovery Education 3M Young Scientist Challenge asked students to create a 1-2 minute video describing a new innovation or solution that could solve or impact an everyday problem related to how we live, how we work or how we play. Ten finalists were chosen for their passion for science, spirit of innovation and communication skills. Here, you can meet the finalists and follow their summer adventures by reading their blog entries!

 

 
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The International Society for Computational Biology (ISCB) announces an international competition to improve the coverage on Wikipedia of any aspect of computational biology. A key component of the ISCB's mission to further the scientific understanding of living systems through computation is to communicate this knowledge to the public at large. Wikipedia has become an important way to communicate all types of science to the public. The ISCB aims to further its mission by increasing the quality of Wikipedia articles about computational biology, and by improving accessibility to this information via Wikipedia. The competition is open to students and trainees at any level either as individuals or as groups.

The prizes for the best article privded by the ISCB will be:

1. 1st prize - $500 (USD) and 1 year membership to the ISCB.
2. 2nd prize - $250 (USD) and 1 year membership to the ISCB.
3. 3rd prize - $150 (USD) and 1 year membership to the ISCB.

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DNA Subway makes high-level genome analysis broadly available to students and educators and provides easy access to the types of data and informatics tools that drive modern biology. Using the intuitive metaphor of a subway map, DNA Subwayorganizes research-grade bioinformatics analysis tools into logical workflows and presents them in an appealing interface.

By "riding" different lines users can:

• Predict and annotate genes in up to 150,000 base pairs of DNA sequence (Red Line).
• Prospect entire plant genomes for related genes and sequences (Yellow Line).
• Determine sequence relationships, view phylogenetic trees and analyze "DNA barcodes" (Blue Line).

Take a ride on DNA Subway, take a look at the manual, or attend a training workshop on how to teach genomics using DNA Subway.

• Play This video on Other link click here

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In early 2013, the Bioinformatics Resource Australia – EMBL carried out a survey of Australian life scientists in order to identify areas in which BRAEMBL could support those researchers to make optimal use of bioinformatics capabilities. More than 200 responses were received from across Australia, representing 750 researchers from all areas of biology.

Overall the picture is of ubiquitous use of the tools and data of bioinformatics, with a clear indication that it is no longer in the hands of specialist bioinformaticians but widely used by laboratory scientists.

Lack of expertise was identified as the single biggest difficulty facing researchers in their bioinformatics activities, and training as the most valuable thing that BRAEMBL could do to support those activities. Dry-lab researchers also highlighted a need for better bioinformatics community networks.

Key conclusions of the survey were:

Bioinformatics is a key activity in Australian research as evidenced not only by the content of responses but also simply by the number of responses

The areas of interest reflect the “central dogma” of molecular biology

Not only bioinformaticians but also laboratory scientists see bioinformatics as core to their work

Geographic location imposes significant but not crippling limitations on exploitation of bioinformatics

Users are more likely to report satisfactory service (hardware, software and support) if it is provided within their own group

There is a very marked concern about lack of expertise and access to expertise in bioinformatics

Training and community building are the most sought after services

There is a significant demand for training of a more general nature, in computer programming and statistics

Survey Background

The Bioinformatics Resource Australia – EMBL (BRAEMBL) was formed in early 2013 as an extension of the Australian EBI mirror project, an initiative designed to remove barriers of geographical remoteness for Australian bioinformatics. BRAEMBL also incorporates the Specialised Facility in Bioinformatics, a National Computational Infrastructure project to make compute resources available to bioinformaticians on a competitive basis.

The evolution to BRAEMBL required a reconsideration of the missions of these projects into three major goals, one of which was for BRAEMBL to enable optimal exploitation of the tools and data of bioinformatics by Australian scientists1. To support this goal, it was necessary to identify the range of bioinformatics activities and needs in Australia, and so the BRAEMBL Community Survey was carried out in an attempt to get as much input as possible from all people who might be users of bioinformatics.

The survey ran throughout February 2013, during which time it was advertised as widely as possible through mailing lists, professional networks, social media, conferences, seminars and websites. Responses were collated and analysed at the end of the month, although the survey has remained active since then to allow a continued opportunity for members of the community to provide input. The survey consisted of a mixture of multiple choice and free text responses, all of which were optional.

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Source:blogs.nature.com

The faculty of the University of California (UC), the largest public research university in the world, have adopted an open-access policy in which they commit to make their research articles freely available to the public.

The policy, adopted on 24 July, was made public by a press release issued on 2 August. It covers 8,000 UC faculty on all ten of the university’s campuses, who commit to grant UC a non-exclusive licence to research articles they author, provide copies of their articles to UC and to make the articles available through Creative Commons licences.

In the press release announcing the policy, Chris Kelty, associate professor of information studies at UC Los Angeles and chair of the UC University Committee on Library and Scholarly Communication, said that the policy “sends a powerful message that faculty want open access and they want it on terms that benefit the public and the future of research”.

The release notes that UC is the latest of more than 175 universities to adopt similar policies. As with policies adopted at other institutions, however, faculty can opt out of the policy or delay the appearance of an open-access version of their work.

That aspect of the policy is controversial. In a 2 August blog post titled ‘Let’s not get too excited about the new UC open access policy’,  UC Berkeley biologist Michael Eisen, a co-founder of the open-access Public Library of Science journals, describes the policy as “completely toothless”.

“[M]any large publishers, especially in biomedicine, are requiring that authors at institutions with policies like the UC policy opt-out of the system as a condition of publishing,” Eisen writes, linking to a list of journals, including Nature, that require faculty to opt out of the Massachusetts Institute of Technology’s open-access policy.

The policy will be phased in over the next year. Faculty at three campuses will begin depositing their work this November. Other campuses will follow suit next November, pending the results of a review of the policy.

Source:blog.revolutionanalytics

If you're an absolute beginner to the R language, this Intro to R video series from Google Developers is a great place to get started. Just download R for your system, start the playlist below, and follow along with the on-screen examples. (The video uses the MacOS X version of R, but you should be able to follow along just fine on Windows as well.)

Each video is between 2 and 4 minutes long, and clearly covers a specific topic about R. The series starts in Section 1 with the absolute basics (entering commands, vectors, variables and arithmetic). Sections 2 and 3 progress to slightly more complex object types (data frames and lists) and programming constructs (loops and flow control). By the time you complete Section 4 you'll be able to write and use your own functions in R. I've embedded the complete series below:

Note that the videos also feature closed captioning, which can be helpful to follow along with new function names and technical terms about R.

If you'd like to take a look at the individual videos in the series, you can click on you tube image.

Source :http://techcircle.vccircle.com

Bangalore-based InterpretOmics India Pvt Ltd, a Big Data startup focused on bioinformatics, has raised Rs 10 crore ($1.6 million) in angel funding from Amarante, a Singapore-based shipping company, and two unnamed Indian investors. The funds will be used for product development, research and marketing.

The company was founded in 2009 by Prahalad H. Achutharao (CEO) and Asoke Talukder (chief scientific officer). Achutharao had earlier worked at Infosys, Verari Systems and other companies. He holds an MS degree in Computer Science from the University of Alabama at Birmingham (US) and a BE degree in Electrical Engineering from Karnataka University. Prior to InterpretOmics, Talukder also worked with several companies such as Sobha Renaissance, Tyfone Communications Development India, Cellnext Solutions, Bluestar Infotech and Mindware.

The startup’s flagship is iOMICS, a cloud-based software platform for aggregating and structuring genomics and biomedical data. Based on semantic technology, the platform makes it easy to manage, process and analyse genomics data – combining them from different sources such as DNA sequencers and other critical clinical databases. It also offers GoHealthyGo, a predictive, preventive, personalised and pervasive healthcare platform that integrates cutting-edge genetic, medical and behavioural knowledge for individuals, physicians, enterprises and institutions that are committed to deliver preventive healthcare.

According to Achutharao, the market for next generation genomics is around $1.6 trillion, but the fact that the company’s offerings are on the cloud, its market opportunity is significantly higher.

Its clientele includes over 17 customers including US-based Joint Genome Institute, Indian Council of Agricultural Research, All India Institute of Medical Sciences (AIIMS) and Biocon, among others. The company is now looking to generate over Rs 350 crore in revenues by fiscal year 2015. Its global competition includes companies like DNAnexus.

Source:

US - The Texas A&M University System Board of Regents on Aug. 8 approved establishment of the Center for Bioinformatics and Genomics Systems Engineering, a joint center of the Texas A&M Engineering Experiment Station and Texas A&M AgriLife Research.

Texas A&M University System Chancellor John Sharp said, "This is a tremendous example of our system’s commitment to new discovery and serving the people of Texas as well as the nation."

The center in College Station will conduct research in bioinformatics, computational biology, genomics and systems engineering as they relate to human and animal health, medicine and agriculture, serving communities across the state of Texas and beyond.

"The Center for Bioinformatics and Genomics Systems Engineering brings together two significant strengths within the engineering and agriculture programs to use bioinformatics and genomics to directly improve the health of animals and humans," said Dr M. Katherine Banks, Engineering Experiment Station director and vice chancellor and dean of engineering at Texas A&M. "With the combined strengths in AgriLife and TEES, this center is poised to become the global leader in the application of bioinformatics, computational biology and systems engineering."

"Joining teams of agriculture and engineering researchers together can only hasten the discoveries that will yield results to improve the lives of people worldwide," said Dr Craig Nessler, Texas A&M AgriLife Research director.

The center will feature 7,000 square feet of state-of-the-art laboratory facilities, a greenhouse and offices for faculty and graduate students.

Dr Edward R. Dougherty, holder of the Robert M. Kennedy ‘26 Chair in the department of electrical and computer engineering at Texas A&M, will direct the center. Dougherty is currently the director of the Genomic Signal Processing Laboratory.

"Our aim is to expand our existing strength in the mathematical formulation of molecular-level medicine and to translate that theoretical capability into diagnostic and therapeutic applications for human and animal health," Dr Dougherty said.

Dr Charlie Johnson, director of Genomics and Bioinformatics at AgriLife Research, will serve as the center’s associate director. Dr Johnson, who has more than 20 years of scientific research and leadership in the biotech industry, launched the AgriLife Research genomics and bioinformatics service core in 2010.

"One of the greatest challenges facing mankind is feeding its ever-growing population," Dr Johnson said. "This center will play a critical role in developing the basic underpinnings and analytical tools to empower the development of improved food and fiber around the globe."

The overall mission of the center is to utilize the strengths in contemporary engineering systems theory and life sciences to perform fundamental and translational research that impacts human and animal health and agriculture and life sciences.

A major component of the center will be training doctoral students and postdoctoral researchers. Within a two-year period the center is expected to have between 25 and 30 doctoral students.

Additionally, officials said the center will:

• Establish a rigorous scientific/mathematical basis of biology to improve understanding of biological systems and apply this knowledge to patient diagnostics and treatment, and to animal and plant sciences.
• Formalize long-term relations within the agricultural and animal science communities in the A&M System, as well as further develop interactions with medical institutions and industry within and outside of Texas.
• Secure significant funding for agricultural and life science research, in particular as it relates to industry within the state of Texas.

We are exploring the DNA, RNA and epigenetic features of single cells in order to better understand normal biology and disease.

Single-cell genomics is the next frontier in molecular biology, offering unprecedented access to study how genetic variability and gene expression impacts on individual cells and cell types. Novel technologies and methods allow us to isolate and analyse the limited genetic material present within a single cell, enabling us to gain a whole-genome view of genetic variability and gene expression at single-cell level.

This field of research is opening up developmental and disease biology. For example, this approach can identify distinct sub-populations of cells within a tumour and reveal how they contribute to cancer development. However, there are significant technical and computational challenges to overcome before this type of research can be carried out in a routine, robust and high-throughput manner.

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learning method survey

Are you involved in teaching bioinformatics or programming to life scientists? If you've identified a learning method* that works for you and that you'd be willing to share with others, we'd like your help! It might be something as simple as using post-it notes to gather input from your trainees, or as complex as a cloud-based mechanism for sharing training materials; we don't mind so long as it's tried and tested and you can summarise it in the following form. We've tried to keep the number of required questions to a bare minimum (5), but the more questions you can answer, the more helpful your response will be to us. You can add as many methods as you like. If you'd like to know what a model answer looks like before you start, you can view one. We're doing this because we want to support course developers and trainers to share learning methods that work for them. This work is being done by the GOBLET trainer-support taskforce (www.mygoblet.org), and will feed into an openly available resource for course developers and trainers in the biomedical sciences that's being developed as part of the EMTRAIN project (www.emtrain.eu). Thank you for your contributions! If you have any questions, please use the 'comments and questions' box at the end of the form. *There are many definitions, but we define a learning method as a set of concepts and procedures for enhancing individual capacity and performance.

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Source: UKGTN website & phgfoundation

The UK Genetic Testing Network (UKGTN)has launched a new website with updated resources.

 

Providing advice to the Department of Health and NHS England on the commissioning of genetic tests within the National Health Service (NHS), the UKGTN promotes the equitable provision of high quality genetic testing services to patients and families. It also coordinates a network of diagnostic laboratories that provides molecular genetic test services, evaluates new tests for their scientific validity and clinical utility, and keeps abreast of new scientific developments that may affect genetic testing.

 

The new website provides an updated search facility (Find a Test) for the UKGTN database of genetic tests services available from the network of laboratories, now including more complex forms of testing such as panels that analyse multiple genes simultaneously. It is possible to compare prices between laboratories, as well as find out more detail about the tests and the criteria for ordering testing via the Gene Dossiers and Testing Criteria sections. The home page provides a sign-up facility to a UKGTN e-newsletter to be published twice a year. 

 

The UKGTN’s work is informed by a diverse and highly expert Clinical and Scientific Advisory Group and four working groups.

 


Check out some new features on Virology.ca:

• Updates to the Base-By-Base tool for analysis of multiple genome alignments
• Includes detailed SNP analysis

This Bioinformatics Resource (Virology.ca, the Canadian half of the now defunct VBRC)  focuses on large DNA viruses:

• Poxviruses
• African Swine Fever Viruses
• Iridoviruses
• Baculoviruses
• Others? Please ask us!

To access the databases and tools, users need an account on Virology.ca. Don’t panic! It’s free and simple, just click register (top right of sidebar) and create a new account if you need one. This is simply to help us keep better track of the usage of our programs so we can better target future development. For more information, email cupton at uvic dot ca.

Our goal is described here; in brief, this site is provided to help with your research! If you use this resource, you must cite the relevant papers, which are found on the individual tool pages (publication list), and please consider collaborative publications.

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