Guest post: It’s an exciting time to be studying human genetics

March 29, 2012 | Posted by Guest in Research |

This is a guest post by Mark Kaganovich, PhD candidate in Genetics at Stanford University and Founder of SolveBio (full bio below). 

It’s an exciting time to be studying human genetics.  Advances in genomic technologies mean that we are rapidly accumulating information about the genetic differences between individuals and across populations. But, how do those differences in A’s, C’s, T’s and G’s become the differences we see in physical traits or susceptibility to disease? The more we learn about modifications and regulation of DNA, RNA and proteins, the more complicated this question is to answer.

I am a doctoral student at Stanford University – I approach the study of genetic variation by integrating computational data analysis with experimental genomics. Essentially, that means we look across genomes, transcriptomes, and proteomes for patterns in the data, form hypotheses about what those patterns might mean functionally for a cell – and ultimately an organism – and then set out to test those hypotheses. The advent of technologies that generate large, informative data sets and the computational infrastructure to learn from the data means that we can generate meaningful hypotheses quickly. The pace of research depends on our ability to test our hunches and move forward to better understand the cellular mechanisms underlying our genomic/proteomic observations.

Setting up high-throughput experiments to confirm or reject computational predictions usually requires specialized equipment and expertise in scaling up individual experiments that no single laboratory can be expected to afford or master in a reasonable time frame.  So for us, collaboration is a natural avenue to explore. We have looked at working with core facilities and companies to do cell culture, microarray work, and sequencing when in-house lab or core facility capacity and scale cannot meet our needs. There are also methods that we are well set up to perform, but often need results sooner rather than later, so a company or core facility can help.

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Guest post: Funding new discoveries with Petridish.org!

March 25, 2012 | Posted by Guest in Research |

This is a guest post by Matt Salzberg, Founder of Petridish.org (full bio below).

If you’re a scientist, you know that funding is becoming harder and harder to find. Traditional sources of funding, such as grants from the National Science Foundation or the National Institute of Health are time intensive, restrictive and slow.  And application success rates have fallen.

That’s why we created Petridish.org – a new tool to help scientists fund worthy projects in need. Petridish is an online community of scientists and everyday science-lovers that allows researchers to connect with private donors interested in their work.

In other fields like art, film, charity and microfinance, we have seen this method of fundraising, known as “crowdfunding,” drive a revolution in the way projects are funded.  Enabled by the mass reach of the internet, projects in these fields have raised hundreds of millions of dollars by pooling the contributions of many to make a large impact. Many of the most notable examples in other fields are sites such as Kiva.org, Donorschoose.org and Kickstarter.com.  In fact, most recently, Kickstarter made headlines when one video game project on their site raised over $2 million from the “crowd.”

So why shouldn’t scientists have a dedicated community too?  The goal of Petridish.org is to provide a platform and community where scientists can promote research, educate and engage the public, and raise money all at once.  Meanwhile, science enthusiasts can donate to projects and be a part of exciting new discoveries.

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Launch of the Science Advocate Initiative

March 20, 2012 | Posted by Team in Company, Science Exchange News |

Our overarching goal at Science Exchange has been to change the pace of scientific research.

Over the past year, we’ve been lucky enough to do just that through our online marketplace for science experiments.  We’ve helped thousands of researchers access service providers across the globe, connect with other researchers around shared resources, and accelerate their productive output through outsourcing deficiencies and focusing on expertise.

But our marketplace has only been one facet of our plans.  Our goals for Science Exchange have been grander, as we continue to roll out new features, programs, and initiatives.  As such, we are happy to announce the launch of our newest program: the Science Advocate Initiative.

Advocates are envisioned as our ambassadors for science, leading a movement to fundamentally transform science.  While our marketplace can serve to lay the groundwork for incremental change, true sustainable change can only emerge from the bottom-up: from the students, postdocs, and professors themselves.

Such individuals will lead the Advocate Initiative, helping to push for infrastructural change in scientific processes.  They’ll engage in peer communications, seminars, conferences, and larger marketing efforts.  They’ll work within their institutions to improve access to shared resources, and open science platforms. They’ll stand at the forefront of a changing dynamic in scientific research, and help make it a reality.

We’ve already launched the Initiative at 5 institutions, including Stanford, Moffitt, UCSF, USC, and Yale.  If you’re interested in becoming a Science Advocate at your institution, check out our Advocate Page for more info.

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Guest post: Finding the perfect antibody

March 15, 2012 | Posted by Guest in Research |

This is a guest post by Alexandra Hodgson, Managing Director of 1DegreeBio (full bio below).

Last year, an estimated $2 billion dollars were spent on research antibodies alone. But in a 1DegreeBio survey of 400 antibody users, 48% reported that at least half the antibodies they purchased did not work as expected. There are many reasons for these reported failures. Some failures may result from a lack of sufficient product information; others might be accounted for by outright user error. Often, however, the antibodies themselves are just not as high quality as they should be – and researchers know it.

Despite these issues, there was no systematic way for feedback about antibody quality to make its way into the user community or back to the companies that provide them. Faced with a bad antibody, most of us just complained to our lab mates and tried a different one. And that’s how my company, 1DegreeBio, was born – to establish the first independent online resource with a comprehensive listing of all academic and commercially available antibodies.

I couldn’t, therefore, resists the opportunity to speak at this year’s annual meeting of the American Biomedical Resource Facilities (ABRF) on a panel titled “The Perfect Antibody: Does it Exist and How Do You Find It?” Leaving aside the question of whether a perfect antibody exists, 1DegreeBio is keenly interested in the problem of how users would find it, if it did.

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Could Outsourcing Experiments Solve Ethical Transport of Lab Mice?

March 15, 2012 | Posted by Elizabeth in Research |

The transport of animals for research can become problematic for a variety of reasons.

The stress placed on animals during transport often necessitate 1-week recovery periods upon arrival at research facilities. Bio-imporation laws complicate matters, where strict AZ quarantine requirements frequently delay access to transgenic strains of mice. And targeting by animal rights groups increasingly complicate transport processes for importing mice, rats, and rabbits species (as noted by the Washington Post yesterday in relation to medical research in the UK).

These issues could be solved fairly easily by outsourcing the experiments instead. Expert specialist laboratories (such as JAX labs) are often better equipped to breed and conduct animal research experiments. Getting animal testing conducted by vet-trained specialists could even improve the treatment of the animals and the experiments themselves, with expert care and handling.

Outsourcing lab work can help not only to improve operational and regulatory compliance with research processes, but also to meet the ethical demands associated with lab and animal research. Yet another reason we’re excited about the work we’re doing at Science Exchange.

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Science Exchange Co-Founder Elizabeth Iorns Receives 2012 Kauffman Entrepreneur Award

March 14, 2012 | Posted by Dan in Science Exchange News |

I’m excited to share that Science Exchange Co-Founder & CEO Elizabeth Iorns has been selected as the 2012 Emerging Postdoctoral Entrepreneur by the Ewing Marion Kauffman Foundation.

The award, sponsored by the Kauffman Foundation and National Postdoctoral Association, recognizes new entrepreneurs who have recently completed or conducted postdoctoral training.

Elizabeth conducted postdoctoral training at the University of Miami’s Miller School of Medicine. Her experiences during her postdoc led her to create Science Exchange in May 2011 to improve the pace and efficiency of scientific research.

We’re excited that the Kauffman Foundation and National Postdoctoral Association have acknowledged Elizabeth (and us) with this award… it is a great boost and an acknowledgement of our goal to improve research collaboration and accelerate support for open innovation platforms.

Most importantly, on behalf of the whole Science Exchange team… congratulations Elizabeth!

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Guest post: C-CAMP – A new model for enabling science in India

March 13, 2012 | Posted by Guest in Core facilities |

This is a guest post by Taslimarif Saiyed, Ph.D., Director and COO of the Centre for Cellular and Molecular Platforms (C-CAMP) (full bio below). 

India has great scientists, but has not achieved maximum output as a community in science, especially in the biological sciences.  One reason has been lack of access to cutting-edge technologies to support scientific talent. A simple example: up until at least the 1980s, common technologies such as RT-PCR and confocal microscopy only arrived in India with a 10-15 year delay. Although this deplorable situation has since improved in select research settings like the National Centre for Biological Sciences (NCBS)the Indian Institute of Science (IISc), the National Institute of Immunology (NII), the Center for Cellular and Molecular Biology (CCMB), and the International Centre for Genetic Engineering and Biotechnology (ICGEB), to name only a few, many excellent scientists who are not fortunate enough to be at premier institutions have remained disadvantaged.

To address this problem, India’s Department of Biotechnology (a federal funding agency) established the Centre for Cellular and Molecular Platforms (C-CAMP) as part of the Bangalore Bio-cluster. Our mandate is to establish cutting edge technology platforms and use them to provide services and training for researchers nationwide. In less than two years, we have been able to establish technology platforms including high-throughput screening, mass spectrometry, next generation genomics, confocal imaging, flow cytometry, a protein technology core and a transgenic fly facility.

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The future of universities

March 12, 2012 | Posted by Elizabeth in Research |

Paul Graham just published a new essay on Frighteningly Ambitious Startup Ideas in which he discusses a number of area that appear ripe for disruption by startups. One of the areas he mentioned was the university system:

Replace Universities. People are all over this idea lately, and I think they’re onto something. I’m reluctant to suggest that an institution that’s been around for a millennium is finished just because of some mistakes they made in the last few decades, but certainly in the last few decades US universities seem to have been headed down the wrong path. One could do a lot better for a lot less money.

The essay has sparked a lot of commentary and debate over on Hacker News, including the following comment by me (view on Hacker News):

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Guest post: Making the most of peer networking

March 8, 2012 | Posted by Guest in Core facilities |

This is a guest post by Susanna Perkins, Director of Research Cores & Operations in the Office of the Vice Provost for Research at University of Massachusetts Medical School (full bio below). 

Seven years ago, I was hired by the University of Massachusetts Medical School (UMMS) to centralize their core facilities management from an operations perspective.  We have 43 core facilities, one of the largest centralized institutional organizations.  Prior to centralization, each was managed from within their home department.  Funding for these facilities flows through the institution, but answering simple questions about how the money was being used was difficult when it involved a dozen different accountants and administrators.  Now that everything is under one organization, we are able to produce quarterly reports that include all the financials, usage, grant support, personnel, etc….  It presents an overview of the entire system, and is also a tool to help us manage across facilities.  For example, if one facility is exceeding revenue projections and will not require as much institutional support, we can offset a less profitable facility with the excess funds.  Centralization allows the institution to utilize our Core funding where it is needed the most – toggling the funding throughout the year as the revenue & expense trends solidify.

I came from the private sector, doing financials for a company producing computer disk drives.  My skillset was an excellent match for this position, which is essentially overseeing the operations of 43 small nonprofit companies.  Because many of the people within core facilities come from a science background, I can assist by bringing business expertise on budgeting, marketing, web sites, and other accounting activities that many science-based Core Directors are more than willing to offload.  This allows the Directors to focus their attention and resources on their technical areas of expertise.

Inevitably, in financially challenging times, my job also entails providing recommendations for the prioritization of funding for facilities.  The Vice Provost for Research makes the difficult decisions, which are weighted by more factors than just profitability numbers, but my work directly informs those decisions.

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Guest post: The rise of contractual conservatism – will it subvert sharing of scientific resources?

March 7, 2012 | Posted by Guest in Core facilities |

This is a guest post by Stephen Byers, Director of the Lombardi Shared Resources at the Lombardi Comprehensive Cancer Center, Georgetown University (full bio below). 

As director of shared resources at Georgetown University’s Lombardi Comprehensive Cancer Center and as Director of the Translation Technologies component of the Georgetown/Howard Univerity CTSA, my goal is to provide our researchers with the highest quality experimental resources, at the best possible price.  Sometimes that means adding in a new technology to our core facilities, sometimes it means reaching out to our CTSA network partners, sometimes it means negotiating with another institution altogether.   One reason I attend the Association of Biomolecular Resource Facilities (ABRF) annual conference is to keep up with cutting edge resources and explore what it makes sense for us expand or introduce as part of our core services and when it makes sense for us to find partners.

Different core facilities develop specializations, driven both by foresight as well as serendipity.   Georgetown, for example, has invested in an outstanding Metabolomics Shared Resource Program.  We’re finding that, in many cases, high throughput analysis of metabolites in blood or urine with LC-Mass Spectrometry is as good as genomic profiling at segregating outcomes in diseases… and a whole lot cheaper.  We can generate as many as 20-30,000 metabolite data points in an hour at $60/hr for 6 samples.  The real challenge for this field, as for much of post-genomic science, is the informatics that goes into analyzing all this data.  Under the guidance of our metabolomics gurus, Al Fornace and Amrita Cheema, and Medical Informatics Director Subha Madhavan, we are improving our informatics services and finding no shortage of investigators eager to take advantage of this technology.

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