OTTAWA, Ontario, April 30 — New Canadian bioinformatics and computational biology research projects will help manage, analyze and interpret vast amounts of genomics data to accelerate advances in personalized medicine, public health and other areas of importance to Canadians and the economy.

"Our government is investing in the technological solutions needed to advance genomics to its full potential for the benefit of Canadians and their families," said the Honourable Gary Goodyear, Minister of State (Science and Technology). "These leading-edge research projects will put Canada at the forefront of innovation globally in the specialized fields of bioinformatics and computational biology."

Through Genome Canada’s 2012 Bioinformatics and Computational Biology Competition, a partnership with the Canadian Institutes of Health Research (CIHR), 17 projects across the country will receive funding.

The mix of large-scale applied and small-scale innovative projects will produce new tools and methodologies to enhance genomics data management and analysis, contributing to improving cancer treatments, quicker responses to infectious disease outbreaks, improved food production, and more. Bioinformatics expands the use of genomics data through the research, development or application of computational tools and approaches. It enables better ways to acquire, store, organize, archive, analyze and visualize data. Computational biology helps make sense of genomics data through computational analysis, modelling, and prediction.

"Managing and analyzing the huge amounts of data generated by genomics technologies is a major challenge. These new projects will offer much-needed innovations that will address this dilemma so that the data can translate into useful genomics applications such as disease treatments, breeding strategies for agriculture, forestry management, bioenergy and aquaculture," said Pierre Meulien, President and CEO of Genome Canada.

"Technological advances in genomics and in high-resolution imaging promise to drastically improve the precision and efficacy of Canadian health care. However, the development of strategies to handle the enormous amounts of data generated from these technologies is essential for us to achieve their full potential. We are proud to be working together with our partners at Genome Canada and the regional Genome Centres in this new initiative in bioinformatics and computational biology that will facilitate research in this critical area," said Paul Lasko, Scientific Director for CIHR’s Institute of Genetics.

The Harper Government's investment in these projects is approximately $6.4 million ($5 million from Genome Canada and another $1.4 million from CIHR). The balance of funding is secured by regional Genome Centres from provincial governments, the private sector and other partners, bringing the total value of these projects to almost $11 million.

To build on Genome Canada’s achievements to date, Economic Action Plan 2013 proposes to provide $165 million in 2014–15 to support Genome Canada’s multi-year strategic plan.

Since 2006, the Harper Government has provided more than $9 billion in new funding for initiatives to support science, technology and the growth of innovative firms, helping to foster a world-class research and innovation system. Economic Action Plan 2013 builds on this strong foundation, helping to position Canada for sustainable, long-term economic prosperity and a higher quality of life for Canadians.

Genome Canada is a not-for-profit organization that invests in genomics research to generate economic and social benefits for Canadians. Genome Canada builds bridges between government, academia and industry to forge a genomics-based public-private innovation enterprise focused on key life science sectors. It develops these partnerships to invest in and manage large-scale research and translate discoveries into commercial opportunities, new technologies, applications and solutions.

Canadian Institutes of Health Research (CIHR) is the Government of Canada’s health research investment agency. CIHR’s mission is to create new scientific knowledge and to enable its translation into improved health, more effective health services and products, and a strengthened Canadian health care system. Composed of 13 Institutes, CIHR provides leadership and support to more than 14,100 health researchers and trainees across Canada. 

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Something we feel strongly about at Nextgenediting is the use of computational biology to support and contextualise the main experimental findings of a biological paper. There is a wealth of primary research that can be performed before you even get started doing your experiments in the lab, and the best papers know how to make the best use of it. These data can be particularly useful for grant applications, too. We sometimes send recommendations back to our biomedical authors saying ‘go to GEO and analyse this dataset - you have all the information available to you tell you exactly what the expression of your gene of interest is in thousands of breast cancers…or colon cancers…or cardiovascular patients….or whatever your disease of interest is’. When you take this approach you often find the experiment you were planning (in vitro or in vivo) has already been performed, or there is supporting mouse data, or often clinical data. They can be used to generate the first figure(s) of the paper, put the experimental data in clinical context, and save a huge amount of time and effort performing costly -omics experiments. If you don’t know how to use these resources or need more information, please contact us.

What we hadn’t realised until very recently was that the same can be done for epidemiological data. We are currently planning our Nextgenediting Global Initiative (for more information click here), and while researching health and income statistics of third-world countries we found the World Bank World Databank. This is a free, online database of Development Indicators, Gender Statistics, and other useful data, which you can mine and interrogate at will for hundreds of different countries - both developed and otherwise. Most exciting for us however, is the Health, Nutrition, and Population Statistics Database which allows you to mine health and disease-related data. You just choose your country or countries of interest, the data series you want, and the range of years you are comparing (from 1961 to present) and the results are presented as tables, graphs, or on a map. You can even download the raw data and work with it yourself to present your own graphs or figures. Truly amazing.

We remember feeling like this when we first realised we could get our hands on raw gene expression data. What a powerful tool to contextualise your own work.

So if, for instance, if you are doing a study on HIV, and you need to know what the AIDS death rates are in various African countries, it would take two minutes to get this chart:

Pasted Graphic

which you can then fully customise. So much better than some outdated and over-cited WHO data, don’t you think? You can then get a first-hand grip on the numbers, trends, and associations relevant to your own research.

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NEW YORK, April 29, 2013 /PRNewswire/ -- announces that a new market research report is available in its catalogue:


BCC Research's goal for this study is to provide a comprehensive analysis of the bioinformatic market by reviewing the recent advances in high-throughput 'omic technologies and computer-enabled technologies that have driven the field forward. It examines the market trends and analysis regarding industry service providers, software solution developers, and IT and bioinformatics service providers that support the pharma industry.

The report's main focus is on identifying the challenges and opportunities that exist in the bioinformatic market following the adoption of high- throughput technologies and the generation of big data. It aims to identify innovative companies and institutes that are extending the boundaries of science and technology to develop innovative solutions and enable knowledge to be extracted from burgeoning data so that it may be put to use for the greater good.


Since the Human Genome Project was completed in April 2003, genome-wide association studies (GWAS) have contributed toward a greater understanding of the genetic basis of complex diseases and advances in high-throughput technologies. This has enabled researchers to rapidly map the genome of vertebrates, invertebrates and pathogens through cost-effective methods.

More recently, improvements in cloud computing capabilities and advances in data-analysis software services have helped to expand the evaluation of available datasets, allowing researchers to build systems biology models of various diseases. Still, the challenge to translate this wealth of information into tangible clinical benefits, to support the development of new therapeutic interventions and to reduce the current prohibitively high cost of drug development remains.


The scope of the study encompasses the global bioinformatic market based on geography, category and application. It provides a detailed analysis of recent advances in 'omic technologies and examines their impact on the bioinformatics market. It discusses the ways in which bioinformatics have been utilized by the pharma and biotech industries to streamline the research and development (R&D) process and improve efficiencies. It provides a detailed analysis of leading countries, companies and technologies that will drive the field forward.


The study provides a detailed analysis of the economic, technological and potential application of bioinformatics; it also examines the market factors and identifies the market potential through the year 2017. The study is aimed at the pharmaceutical industry, biotechnology firms, research laboratories and individuals interested in exploiting the commercial opportunities offered in this field.


Both primary and secondary sources were used in preparing this study. This analysis of bioinformatics breaks down the market by geography, category and application, and also analyzes current and potential opportunities for bioinformatic business. It includes market sizes from 2011 and forecasts market revenues through 2017.

Primary research involved e-mail correspondence and telephone interviews for each market, category, segment and sub-segment across geographies. BCC Research extends its thanks those who took part in interviews for this report, especially the following, who gave so generously of their time:
Paul Clemons , PhD, Director of Computational Chemical Biology Research Broad Institute, U.S.
Rolf Apweiler, PhD, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, U.K.
John Atack , PhD, Translational Drug Discovery Group, School of Life Science, University of Sussex, U.K.
Tom Schwei , Vice President, CFO and General Manager DNASTAR Inc., U.S.
Simon M. Lin , MD, Editor-in-Chief at the Journal of Computer Science and System Biology, BIRC, U.S.

Secondary research was performed on internal and external sources to acquire qualitative and quantitative information for this report. These sources include:
• Company websites, annual reports, financial reports and investor presentations.
• Industry trade journals, scientific journals and other technical literature.
• Relevant patent and regulatory databases.
• National government documents, statistical databases and market reports.
• News articles, press releases and webcasts specific to the companies.


Dr. C.L. Barton has more than 10 years' practical pharmaceutical research experience with a leading pharmaceutical company and has served as a Pan-European Pharmaceutical analyst with a European bank. Dr. C. L. Barton Ltd. aims to provide independent, tailor-made, pharmaceutical thematic research to investment houses. Research reports combine independent scientific analysis with patients- and prescription-based models to forecast the potential sales growth of key developmental drugs and to isolate the key drivers within the pharmaceutical sector.


The report provides:
• An overview of the global market for bioinformatics.
• Analyses of global market trends, with data from 2011 and 2012, and projections of compound annual growth rates (CAGRs) through 2017.
• Technological descriptions and patenting trends in bioinformatics.
• Examination of the economic environment affecting the deployment of bioinformatics.
• Discussion of other influential factors, such as R&D spending in the pharmaceutical sector, the growth of agrobiotechnology, and the expanded use of microbial genomics.

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Qlucore, a world leader in the development of bioinformatics software, today announces it will develop an enhanced NGS-enabled release of Qlucore Omics Explorer. A recent grant awarded by VINNOVA, the Swedish Governmental Agency for Innovation Systems, now makes it possible for Qlucore to implement its NGS solution.
Genome research has advanced significantly in recent years, and the ability to determine the entire DNA of a person for $1,000 will soon be reached. This technological revolution, known as "Next Generation Sequencing" (NGS), will be a paradigm shift for biomedical research, industry and healthcare. This shift will move the bottleneck from data generation to data analysis and interpretation. Qlucore is at the forefront of commercial software development for the analysis of genomic data sets. The firm has an impressive customer base, including several of the world's largest pharmaceutical companies and prestigious international research institutions, in more than 20 countries.
Qlucore will extend it’s current Omics Explorer platform with a new product module for the fast, user-friendly and interactive analysis of NGS data. The product module will be for users such as biologists and scientific researchers, and will differ from other solutions currently on the market, as existing solutions typically require an experienced data analyst or bioinformatician.. Qlucore's unique approach makes it possible for more users to perform analysis themselves, and increases the likelihood of innovative and better results both within the scientific research and healthcare fields. Development and innovation will be driven by Qlucore in cooperation with world leading scientists at Sweden's Lund University.
“Qlucore Omics Explorer is currently aiding scientists around the world to visually analyze a wide range of data types from genetic and protein related experiments. With this support from VINNOVA we will give scientists the same user experience for NGS data analysis. We will deliver a new and powerful user analysis experience.” says Carl-Johan Ivarsson, President, Qlucore
VINNOVA is the Swedish Governmental Agency for Innovation Systems, and a major part of its support for small and medium-sized enterprises (SMEs) is the Research&Grow programme which now includes Qlucore. One of VINNOVA's strategic areas is supporting innovative SMEs.
“Small and medium-sized enterprises (SMEs) are characterized by an ability to accept, apply and develop new knowledge and techniques in new business opportunities. This is how they strengthen their competitiveness and growth prospects. VINNOVAs Research&Grow program is designed to strengthen and stimulate growth in SMEs through increased Research and Development.” says Carl Naumburg, Program Manager at VINNOVA.  
Qlucore will build on its interactive data visualization and make it available for NGS data in future versions of Qlucore Omics Explorer. Qlucore plans to release a first NGS enabled version of Qlucore Omics Explorer in 2014.

Carl-Johan Ivarsson, MSc, is a co-founder and CEO of Qlucore.  He has more than 15 years' experience in the international software, data analysis and telecommunication industries, in both business management and sales, including two years as the head of Ericsson Mobile Platforms in China and six years as Qlucore President.
About Qlucore
Qlucore started as a collaborative research project at Lund University, Sweden, supported by researchers at the Departments of Mathematics and Clinical Genetics, in order to address the vast amount of high-dimensional data generated with microarray gene expression analysis. As a result, it was recognised that an interactive scientific software tool was needed to conceptualise the ideas evolving from the research collaboration.
The basic concept behind the software is to provide a tool that can take full advantage of the most powerful pattern recogniser that exists - the human brain. The result is a fast, user friendly and powerful software program that lets the user handle and filter data and the same time instantly visualise it in 3D. The application areas span multiple fields with the common factor that large sets of numerical data need to be analysed. Over the last five years major efforts have been made to optimise the early ideas and to develop a software program that is extremely fast, allowing the user to explore and analyse high-dimensional data sets with the use of a normal PC, interactively and in real time.
Qlucore was founded in early 2007 and the first product was released the same year. The latest version of this software, called Qlucore Omics Explorer, is a major step in providing researchers an easy to use and still powerful tool for analysis of large numerical datasets. The combination of best in class visualization, fantastic speed and advanced statistics support and user friendliness puts the user in focus and supports instant analysis and creativity., The visualization methods range from an innovative use of principal component analysis (PCA) to interactive heat maps and flexible scatter plots. All user action is at most two mouse clicks away. The company's early customers are mainly from the Life-science and Biotech industries and they use Qlucore Omics Explorer on gene expression data, protein data, DNA methylated data, micro RNA data and other genomic data. Please read examples of our peer reviewed publications in scientific journals. 
VINNOVA - Swedish Governmental Agency for Innovation Systems - is Sweden’s innovation agency. Its mission is to promote sustainable growth by improving the conditions for innovations, as well as funding needs-driven research.
VINNOVA’s vision is for Sweden to be a world-leading country in research and innovation, an attractive place in which to invest and conduct business. It promotes collaborations between companies, universities, research institutes and the public sector. It does this by stimulating a greater use of research, by making long-term investment in strong research and innovation milieus and by developing catalytic meeting places. VINNOVA’s activities also focus on strengthening international cooperation. In order to increase impact, it is also dedicated to interacting with other research financiers and innovation-promoting organisations.
Every year VINNOVA invests about SEK 2 billion in various initiatives. Since co-financing must total at least the same amount, funds have more than doubled. Funding decisions are made with assistance from national and international experts and there is ongoing monitoring and evaluation of all initiatives. It carries out regular impact analysis to evaluate and draw lessons from the long-term impacts of VINNOVA’s efforts.
VINNOVA is a Swedish government agency working under the Ministry of Enterprise, Energy and Communications and acts as the national contact agency for the EU Framework Programme for R&D. About 200 people work at VINNOVA´s offices in Stockholm and Brussels.

Press Contact:                  Andrew Ball/ Alison Scarrott                  Chaz Brooks Communications Ltd (CBC)                                                     
Tel: +44 (0)1483 537 890 Email:  [email protected] / [email protected]  Web:
Qlucore Contact:  Twitter: @Qlucore    Phone: +46 46 286 3110
This information was distributed by Cision
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Duration: 5 days lecture & practical workshop
Scientific Organizers: Allegra Via (Uni. La Sapienza, Rome) & Vicky Schneider (TGAC)
When: 7-11 October 2013
Registration: £150 (includes tea/coffee, lunch and one course dinner), limited spaces available.

REGISTER HERE Deadline 10 July 2013

Aims: Python is an object-oriented programming language that is ideal for biological data analysis. The course will start with very basic language concepts and instructions and will cover all the main language aspects, including variables, types, modules, functions, exceptions, control of flux, input, output, and classes. All the examples and practical sessions will focus on solving particular biological problems. In particular, examples and practical sessions will cover:
- working with DNA and protein sequences
- data retrieval from files and their manipulation
- running applications, such as BLAST, locally and from a script
- finding motifs in sequences
- parsing Swiss-Prot files, PDB files, ENSEMBL records, blast output files, etc.

Biopython will be also introduced and applied to some of the mentioned examples.
The course is meant to be highly interactive and the students will continuously put theory into practice while learning.
By the end of the course, the students will have a good understanding of Python basics and will have acquired the skills to manage any type of bioinformatics record and to run applications from scripts.
Unix/linux basic skills will be provided at the beginning of the course.
Course Pre-requisites
Basic familiarity with bioinformatics data resources such as Uniprot/Swiss-Prot, Blast, ENSEMBL, PDB, etc. The course is directed to biologists with little or no programming experience and aims at making them capable to use Python to autonomously manage and analyse biological data.

Target Audience
End-users of bioinformatics databases and tools that aim at developing hands-on capabilities for biological data analysis, ie writing their own or adapting somebody else's Python scripts in an autonomous way.


Allegra Via graduated in Theoretical Physics at Sapienza University of Rome and obtained her PhD in Cellular and Molecular Biology in 2002. Since 1998 she works in Computational Biology and regularly teaches Bioinformatics and Python Programming Language to bioinformaticians and biologists. She was Postdoctoral Fellow at the University of Rome 'Tor Vergata' where she has been Adjunct Professor in 2005-2010. Since the academic year 2010-2011 she teaches at Sapienza University of Rome. She also gives invited lectures in other universities and in training courses (e.g. GTPB). Currently she works as researcher in the Biocomputing Group of Sapienza University of Rome headed by Anna Tramontano. Her main research interests include protein structural bioinformatics and protein function prediction and analysis. Besides her research activity, she wrote two book chapters related to Internet for Cell and Molecular Biologists.

Affiliation: Sapienza Università di Roma, Roma, IT

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SV Angel, one of the Valley’s best-known early-stage firms, says it’s starting to look heavily at health startups that take a “software-first approach” towards human biology, medical research and patient care.
The firm has always had a list of six to eight “megatrends” that it invests prolifically in. Right now, those are big data, social commerce, online-to-offline commerce, education tech, the sharing economy and the “Internet of things.” Now they’re adding “health informatics” to that list.
By that, SV Angel is looking for startups that “use software, IT and data science to help diagnose, treat, reduce and cure disease – at the physical, mental and emotional levels.” It’s a broader definition than just bioinformatics, because it encompasses medical records and other types of patient data.
Managing director David Lee, who is a cancer survivor, said that the firm finally feels comfortable with the idea that software is about to eat healthcare.
“I’m not a biologist. I don’t invest in biotech companies. We’re software investors first and foremost,” he said. “But the more I learned about bioinformatics and health records, the more I felt that the timing was ripe.”
A couple things are feeding into this. For one, the costs of genome sequencing are falling dramatically. The cost of sequencing a full human genome has gone from $100 million in 2001 to $8,000 today — even faster than Moore’s Law. Secondly, there are meaningful governmental and financial incentives to move toward electronic medical records. (It’s also just common sense to move away from paper records.)
He pointed to investments in companies like Counsyl (which I profiled earlier this week), Benchling and medical records startups like Elation EMR and Practice Fusion. There are also younger startups like Medisas, which is building software to help with patient hand-offs and transfers.
A few other firms like Founders Fund, Khosla Ventures and Felicis Ventures have carved out reputations over the past few years for aggressively investing in health tech. Note that no one here is backing companies that require an expensive, 10-year drug testing cycle overseen by the FDA. All of these firms tend to look for companies that have less regulatory risk, like in the medical devices space or with diagnostics and bioinformatics (although Founders Fund has done a few deals in FDA-regulated therapeutic biotechnology if they felt comfortable with the team and opportunity).
SV Angel has been one of the most prolific backers of social networking, real-time, mobile (and yes, even SoLoMo) startups over the past few years. So are they eating their words?
“People might say that consumer’s not hot again, but we’re still going to invest in consumer startups,” Lee said. “We don’t try to time the market.”
Lee explained the firm’s thinking behind its new focus in a blog post today:
We at SV Angel invest in “megatrends.” We pick 4-6 investment themes and invest heavily in each one. Some of these trends include: real-time data, online-to-offline consumption, social commerce, collaborative consumption, education and the internet of things.
We believe that there is a massive opportunity in the intersection of software and biology, which we broadly define as “Health Informatics.” This term has a formal definition but we tweaked it to make our own. It is a software-first approach to solving problems in human biology, medical research and ultimately, patient care. We think the timing is right for software developers to make an impact in these areas. The ultimate goal is to use software, IT and data science to help diagnose, treat, reduce and cure disease – at the physical, mental and emotional levels. If we see a bright founder working in this area, the opportunity will move to the “top of the pile” as if it’s in one of our other preferred trends.
The catalyst of this trend is the cheap, abundant data of two types – medical and molecular data. Cheap, abundant data combined with new ways of measurement and analysis leads to technological breakthroughs. There will be a flood of medical data driven by electronic medical records and the like. For example, the recentAffordable Care Act (i.e., “Obamacare”) basically pays doctors for complying with a federal mandate to move from paper to software-based solutions. By 2024 or so, every hospital will move to electronic records. Right now, it’s estimated that only 2% of hospitals comply with this law. Thus in ten years, the amount of data will increase 50X.
On the molecular front, the costs of sequencing technology is falling almost 5x faster than Moore’s Law. (The interpretation and analysis of the data lags this trend but is improving as well.) President Obama also recently announced a major national initiative to map the human brain in the same way that human genome was mapped back in the early 1990′s. This is just another example of “offline” or analog data being digitized and accessible to coders.
Google motivated a generation of bright computer scientists to learn the ins-and-outs of the advertising industry and turn it into a software problem. The original PayPal founding team went through the schlep work of learning the norms, regulations and other vagaries of the payment industry in the early 2000′s. And they used software to help re-invent it. And most recently, Palantir went through the hard, unsexy work of understanding the intelligence and defense industries and used software to attack hard, important problems. We want to back founders who want to do the same when it comes to health informatics.
We are already working with and investors in founders and companies in this area. Those include Counsyl, Benchling, Practice Fusion, ElationEMR, DNA Nexus, Medisas and Flatiron. Counsyl in particular is a flagship company. They were featured yesterday inTechCrunch. The founding team has a traditional computer science background. In fact, they even started the company thinking they were going to be a pure software shop. Ultimately, they built a lab using cheap, commodotized hardware – a trend that wasn’t in vogue then but is now. Ramji Srinivasan, the CEO of Counsyl, is the archetype of what we will look for. He will be an advisor to us on this effort.
Another advisor is Professor Atul Butte, a Stanford University School of Medicine professor, researcher and entrepreneur in medical bionformatics. He has been a thought leader and pioneer in the area of applying computer and data science to biomedical research. He is a sounding board and inspiration for us to pursue this trend and we’re thrilled to have him with us as we learn more about this fascinating area.
But perhaps the most critical advisors to us will be Jeremy Richman and Jennifer Hensel. They are scientists and lost their only child, Avielle, in the Newtown shooting. They courageously set up the [Avielle Foundation}( to use science and technology to help understand why these tragedies happen. They encouraged us to think more holistically about how to reduce gun violence and how to use technology to identify and treat the root causes of these tragedies. Biomedical research, bioinformatics and brain health are all areas that need further investigation to understand the “why” as well as the “how.” Great software companies and entrepreneurs can play a fundamental role here.
On a personal front, I am a cancer survivor so I have a selfish reason to accelerate this vision. Scientists are more confident than ever that genetic mutations play a huge role in why cancer happens. I believe that great software companies in the mold of Google, PayPal and Palantir will help make cancer a chronic condition and quite possibly, cured.
To be clear, while this megatrend has philanthropic and personal benefits, this is not a philanthropic or personal venture. We believe this is a massive market opportunity for young hackers and founders. And we want to be crystal clear that this effort is consistent with our historical focus – great founders using software to address new and large markets.
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