A new paradigm for drug discovery: part one – how the information age is transforming biological research
Dr Kevin Lustig and Dr Maria Thompson
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Assay Depot
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In part one of four, Dr Kevin Lustig and Dr Maria Thompson discuss the changing face of drug discovery and development and life science research in general.
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Outlining a process for research in the information age allows scientists to overleap the competition and accelerate their research projects as never before by tapping into all of the resources now available online. Using specific examples from scientists that have already embraced the power of public information, outsourcing, and crowdsourcing to make real discoveries and develop real products using virtual resources. These resources are available to all of us if you just know where to look.
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"The advent of the information age has caused a ground shift in the way in which research can be performed..."
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The cycle below shows the new path of research from ideation to results. In this series, we will examine each of the elements in turn and show how science is open for business as never before.
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Figure 1: Cycle showing the new path of research from ideation to results.
Part I of IV: Using online data to generate new ideas
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The advent of the information age has caused a ground shift in the way in which research can be performed, and some cutting edge scientists are taking advantage and riding the wave to new discoveries.
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Once the sole purview of large multinational corporations and academic institutions, the availability of information, the ability to find like minded others, and the ability to share your results with a whole online community has led to a democratization of scientific research.
• Scientists can now access the results of other scientists and use 3rd party data to find that one brilliant idea.
• Any one of us can reach out to the public at large and ask for funding through the power of crowdsourcing.
• You can obtain clinical samples from one vendor and have another perform testing on them, effectively performing wet lab work without ever setting foot in a lab.
• Finally, you can share your results online for all to see.
The new age of science is upon us, and the only question left to answer is this: are you an innovator? An early adopter? Or a laggard?
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"Since the start of this century there has been a quiet explosion in the amount of scientific data available online."
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Mining online data to generate your own good ideas
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Since the start of this century there has been a quiet explosion in the amount of scientific data available online.
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Figure 2: The number of gene-expression data sets that are publicly available online over the past ten years. (Source: Gene data to hit milestone. Nature News. 18 July 2012)
Slowly but surely, a mass of raw scientific data has become available. Huge research funding bodies such as the NIH have started to require that the raw data sets from any research funded by them be made public, available for download by anyone with a laptop and a WiFi connection.
“The last 10 years have seen a massive increase in the amounts of Open Access publications available in journals and institutional repositories. The open presence of large volumes of state-of-the-art knowledge online has the potential to provide huge savings and benefits in many fields.”
Petr Knoth, the Open University Core Project.
Work smarter, not harder
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This data represents a huge treasure trove of information on all manner of topics. In fact, so vast is the data set that it now makes sense for almost any scientist embarking on a new project to start here, asking the question, “is there anything in here I can use to get me started?” This sort of ‘work smarter, not harder’ thinking has the potential to reduce cost and leapfrog the savvy researcher forward, potentially relieving them of the costly and time consuming need to generate data themselves if others have already done it for them.
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Reaching critical mass
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Of course scientists have long understood the importance of taking time to read the literature and find out everything they can about a particular issue before embarking on bench work of their own. But it is only in recent years, as the amount of free data has continued to expand, that we have hit true critical mass. Enabling some forward-thinking researchers to not only get a leg up in reducing the amount of bench work they need to do themselves, but to leap frog the wet lab work completely and make new discoveries using only the freely available data, their lap top, and some simple spreadsheet software.
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"This sort of ‘work smarter, not harder’ thinking has the potential to reduce cost and leapfrog the savvy researcher forward..."
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Virtual discovery – tangible results
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Exploiting the freely available scientific data enabled a team working on pediatric cancer, led by Dr. Purvesh Khatri at Stanford University, to develop new diagnostic tests for cancer using almost no unique data. All of their analysis was done on other people’s data sets downloaded from the NIH data repository. Yet within this data they were able to find previously hidden gems in the form of potential biomarkers for cancer, some of which they took forward into testing and refined into diagnostic tools for predicting the disease state of new patients. It is worth mentioning here that not only did they find the biomarkers thanks to online data, but they also tested them and developed the diagnostics tests in a wholly outsourced fashion, never setting foot in a laboratory themselves.
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“We don’t do wet lab experiments for discovery,” says Khatri. “Those are for validating hypotheses”.
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What next?
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In the second part of this series, we’ll look at the next step in the cycle and discuss how to test your hypothesis. We will show how other scientists have successfully bypassed the grant application process, looking past the major funding bodies and instead obtaining their funding from the public at large through the power of crowdsourcing.
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References
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If you’re interested in expanding your own horizons and taking advantage of the wealth of public data, below are a few great resources to get you started:
• CORE (COnnecting REpositories) www.core.kmi.open.ac.uk/search
• NCBI: www.ncbi.nlm.nih.gov
• For a full list of online data repositories in any field see Wikipedia: http://en.wikipedia.org/wiki/List_of_academic_databases_and_search_engines
You can view part two in this series here
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About the authors:
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Kevin Lustig is co-founder and CEO of Assay Depot, the world’s largest online marketplace for scientific services. In 2001, he founded Kalypsys, a drug discovery company that raised over $170 million in venture capital. Prior to this, he directed lead discovery at Tularik, a biopharmaceutical company purchased by Amgen in 2004 for $2.5 billion. Kevin has over 30 years of research experience including a postdoc at Harvard Medical School and a PhD degree in biochemistry from UCSF. His research discoveries have been published in Science and Nature magazines and he has been awarded eight technology patents. Dr Lustig can be contacted at klustig@assaydepot.com and more information about Assay Depot can be found at www.assaydepot.com
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Dr Maria Thompson is a molecular biologist with over 16 years of experience in research and development for pharmaceuticals and diagnostics. Over this period she has held a variety of leadership positions including Head of Genome Wide Screening for Type 2 diabetes, Six Sigma Black Belt, and VP of Scientific Affairs. Dr Thompson is currently Principal Consultant at APEX think, a niche consulting company providing scientific and technical advisory services to clients across the life science industry. Dr Thompson holds a BSc in Genetics and a PhD in Molecular and Cellular Biochemistry from the Royal London School of Medicine, UK. She can be contacted at: consulting.mt@gmail.com or www.APEXthink.com
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How can you use online clinical data to generate new ideas?
