The Importance of Replication Studies

July 28, 2016 | Posted by Team in Company, Reproducibility, Research, Science Exchange News, Uncategorized |

My TEDMED talk about scientific reproducibility was released today, so I wanted to take the opportunity to provide some additional thoughts about the importance of replication studies.

Every year, billions of dollars are spent funding biomedical research, resulting in more than one million new publications presenting promising new results. This research is the foundation upon which new therapies will be developed to enhance health, lengthen life, and reduce the burdens of illness and disability.

In order to build upon this foundational research, these results must be reproducible. Simply put, this means that when an experiment is repeated, similar results are observed. Over the last five years, multiple groups have raised concerns over the reproducibility of biomedical studies, with some estimates indicating only ~20% of published results may be reproducible (Scott et al. 2008, Gordon et al. 2007, Prinz et al. 2011, Steward et al. 2012, Begley and Ellis 2012). The National Institutes of Health (NIH), the largest public funder of biomedical research, has stated, “There remains a troubling frequency of published reports that claim a significant result, but fail to be reproducible. As a funding agency, the NIH is deeply concerned about this problem”.

Despite the growing concern over lack of reproducibility, funding for replication studies, the only way to determine reproducibility, is still absent. With no funding systematically allocated to such studies, scientists almost never conduct replication studies. It would be interesting to obtain the exact numbers, but it appears that last year the NIH allocated $0 to funding replication studies, out of a $30B+ budget. In the absence of replication studies, scientists end up wasting precious time and resources trying to build on a vast, unreliable body of knowledge.

It is easy to see why funders might shy away from funding replication studies. Funders want to demonstrate their “impact,” and it is tempting for them to solely focus on funding novel exploratory findings that can more easily be published in high profile journals. This is a mistake. Funders should instead focus on how to truly achieve their stated goals of enhancing health, lengthening life, and reducing the burdens of illness and disability. Although allocating a portion of funding towards replication studies would divert funds from new discoveries, it would enable scientists to efficiently determine which discoveries were robust and reproducible and which were not. This would allow more rapid advancements by allowing scientists to build upon the most promising findings and avoid wasting their time and funding pursuing non-robust results.

Some researchers find the idea of replicating previous studies unnecessary or even offensive. However, it is the responsibility of the scientific community, including funders, to work as quickly and cost effectively as possible to make progress. Introducing replication studies as part of the process provides an effective way to enable this.

If you would like to see funding specifically allocated for replication studies, please register your support. We will share this information with funders in the hope that it will encourage them to establish funding programs specifically for replication studies to improve the speed and efficiency of progress in biomedical research.

by Elizabeth Iorns, Ph.D.

CEO and Co-Founder

Science Exchange

About Science Exchange

 

Science Exchange is the world’s leading marketplace for outsourced research. The Science Exchange network of 3000+ scientific service providers has run the experiments for the major replication studies that have been conducted to date including the largest biomedical replication study undertaken (Reproducibility Project: Cancer Biology). Additional details are available here: https://www.scienceexchange.com/applications/reproducibility

 

References

  1. https://www.nih.gov/about-nih/what-we-do/budget#note
  2. http://www.ncbi.nlm.nih.gov/pubmed
  3. https://www.nih.gov/about-nih/what-we-do/mission-goals
  4. Scott et al. Amyotroph Lateral Scler. 9, 4-15 (2008)
  5. Gordon et al. Lancet Neurol. 6, 1045–1053 (2007)
  6. Prinz et al. Nat Rev Drug Discov. 10, 712 (2011)
  7. Stuart et al. Experimental Neurology 233, 597–605 (2012)
  8. Begley and Ellis. Nature. 483, 531-3 (2012)
  9. http://www.nature.com/news/policy-nih-plans-to-enhance-reproducibility-1.14586
  10. http://www.nature.com/news/reproducibility-the-risks-of-the-replication-drive-1.14184

 

 

Science Exchange Acquires OnDeckBiotech to Expand Scientific Services Marketplace in Biotech Industry

June 7, 2016 | Posted by Team in Company, Science Exchange News, Uncategorized |

Science Exchange, the world’s leading marketplace for scientific research, announced today that it has acquired OnDeckBiotech, an international community and marketplace that connects biopharmaceutical companies with contract service providers. The acquisition brings together two of the major platforms for outsourced scientific services, and strengthens Science Exchange’s market-leading position by significantly increasing its global network of contract research organizations, core facilities, and other scientific service suppliers.

“Over $40B a year is spent on outsourced scientific research by the top 50 pharmaceutical companies alone, and much of this spend is highly fragmented across thousands of individual scientific service suppliers. Platforms for outsourced scientific services, like Science Exchange and OnDeckBiotech, solve the challenges associated with this fragmentation by providing scientists with efficient access to a diverse network of qualified suppliers under a single relationship,” said Dr. Elizabeth Iorns, Co-founder & CEO of Science Exchange. In praising the fit of the two companies, Iorns added, “OnDeckBiotech has developed a number of strategic relationships with industry groups and research foundations which complement the direct channels Science Exchange has developed with biopharmaceutical, government, and academic researchers.” OnDeckBiotech’s relationships, which include MassBio through the MassBio Gateway, the Biotechnology Innovation Organization (BIO) through BIO BizLink, and the Alzheimer’s Drug Discovery Foundation (ADDF) through ADDF ACCESS, will continue to be supported by Science Exchange as part of its strategy to become the ubiquitous platform for scientific outsourcing across all disease areas and stages of research and development.

As part of the acquisition, Science Exchange will take over OnDeckBiotech’s office in Cambridge, MA, giving Science Exchange a physical presence in two of the world’s largest and fastest growing biotech research clusters. “Science Exchange already works with 8 of the 10 largest pharmaceutical companies, many of which have invested heavily in these two clusters.  Now with offices in Palo Alto and Cambridge, in addition to Account Managers operating remotely in San Diego, New York, and other core markets, our team is uniquely positioned to help researchers inside these organizations access the world’s leading scientific service providers and most innovative scientific technologies,” said Iorns.

OnDeckBiotech’s Founder & CEO, Cliff Culver, will join Science Exchange as VP, Strategy and General Manager, Boston as part of the acquisition. “Cliff has been a visionary in the outsourced scientific services space, and we’re incredibly excited for him to join our team and continue our joint mission of enabling better, faster, and more efficient scientific collaboration,” said Dan Knox, Co-founder & COO of Science Exchange. Culver added, “We can’t wait to get started working with Science Exchange. The industry consistently reports that time and effort spent identifying and managing outsourced contracts hurts research productivity. Our companies have each demonstrated the value we can create by addressing these challenges, and our combined platforms and networks are uniquely positioned to continue to lead the market.”

Iorns concluded, “The total transactional volume of experiments conducted through the Science Exchange platform grew over 500% in 2015, and the OnDeckBiotech acquisition will further accelerate our already remarkable growth in 2016.”

About Science Exchange

Since its founding in 2011, Science Exchange has become the world’s leading marketplace for scientific research. Through Science Exchange, researchers can securely access a network of 1,000s of screened and verified contract research organizations (CROs), academic labs, and government facilities that are available to conduct scientific experiments. Science Exchange has been used by researchers from over 2,500 different companies and organizations, including many large pharmaceutical companies and government research facilities like the NIH, the FDA, and NASA. The company’s mission is to enable breakthrough scientific discoveries by providing researchers with easy access to the world’s best service providers. To date, the company has raised over $30 million from Maverick Capital Ventures, Union Square Ventures, Index Ventures, OATV, the YC Continuity Fund, and others.

Science Exchange Announces $25 Million in New Funding Led by Maverick Capital Ventures

March 23, 2016 | Posted by Team in Company, Science Exchange News, Uncategorized |

Science Exchange, the leading marketplace for scientific research, announced today that it has raised $25 million in new funding. The latest funding round was led by Maverick Capital Ventures and also included participation from Union Square Ventures, Index Ventures, YC Continuity Fund, Sam Altman, and others.

Since its founding in 2011, Science Exchange has become the world’s leading marketplace for scientific research services. The company provides secure access to a network of 1000s of screened and verified contract research organizations (CROs), academic labs, and government facilities that are available to conduct experiments on the behalf of scientists. The Science Exchange platform has been used by scientists from over 2,500 different companies and organizations. The company has experienced significant growth in the last 12 months, including seeing the total transactional volume of experiments conducted through the Science Exchange platform grow over 500% in 2015.

“Over $40B a year is spent on outsourced scientific research by the top 50 pharmaceutical companies alone. Much of this spend is highly fragmented across thousands of individual scientific service suppliers, and this fragmentation represents a challenge to both individual scientists and sourcing procurement departments,” said Dr. Elizabeth Iorns, Founder & CEO of Science Exchange. “The Science Exchange platform solves this challenge: we provide scientists with efficient access to a diverse network of qualified suppliers under a single relationship, and at the same time we provide sourcing departments with more information and control over their outsourcing spend.”

8 of the top 10 pharmaceutical companies now use Science Exchange, viewing it as a way to efficiently access innovative external resources. Science Exchange also helps tackle one of the most significant challenges facing the highly-trained researchers at these companies: time and resources spent identifying and managing outsourcing contracts. James Lillie, VP In Vitro Biology at Genzyme (a Sanofi company), was recently quoted as saying, “We now look at the Science Exchange as the best way of finding new outsourcing opportunities with collaborators and CROs. We’re shifting more of our efforts for new outsourcing contracts there.”

As part of the Series B, Maverick Capital Ventures Managing Partner David Singer (former Founder/CEO of Affymetrix, GeneSoft Pharmaceuticals, and Corcept Therapeutics) will join the company’s board. “We spent a lot of time evaluating the growing market for outsourced scientific services. We concluded first, that there is an expanding market need for a marketplace to aggregate the thousands of suppliers, and second, that Science Exchange is poised to become the ubiquitous platform for scientific outsourcing,” said Singer.

Andy Weissman, Partner at Union Square Ventures, who has been on the company’s board since 2013, agrees. “With over 500% growth in marketplace transaction volume in 2015 and some companies already spending over $1M each month on the platform, Science Exchange is the clear market leader,” said Weissman.

Science Exchange is headquartered in Palo Alto, CA, and has clients, including many large pharmaceutical companies, around the globe. The company has now raised over $30 million and plans to use the new funding to expand its team in all areas including product, engineering, sales, marketing, and customer success. The full list of investors in the latest round is Maverick Capital Ventures, Union Square Ventures, Index Ventures, OATV, YC Continuity Fund, Windham Venture Partners, Collaborative Fund, Fenwick & West, Jose Suarez (CEO of TEDMED), Sam Altman, Steve Case, Kal Vepuri, Jenny Haeg, Alexander Levy, Paul Buchheit, and Silicon Valley Bank.

 

 

 

A Voyage Through the PacBio Genome Galaxy

March 16, 2016 | Posted by Team in Science Exchange News |

We are pleased to support the Genome Galaxy Initiative from PacBio. SMRT Sequencing Technology manufacturer PacBio recently unveiled the Genome Galaxy Initiative. The Genome Galaxy Initiative, based on the Experiment platform, supports expedited, open-access genomic projects. It’s a central location for SMRT Sequencing-based projects seeking crowdfunding, and fosters a community of scientists and patrons interested in asking research questions that can only be answered with long-read sequencing. As high-quality genome assemblies from the PacBio RS II and the Sequel System have become even more affordable and accessible, partnering with Experiment is a great fit. Through this program, even more scientists will have access to the most comprehensive view of genomes, transcriptomes, and epigenomes from SMRT Sequencing.

The Genome Galaxy Initiative

One of the initiatives flagship participants is the Kakapo 125 Project. An effort to sequence the genomes of every individual in the entire kākāpō species. This project was made possible thanks to the high quality reference genome generated by Dr. Jason Howard at Duke’s Jarvis Lab using SMRT Sequencing technology.

Kakapo Jasira

Other projects in the Genome Galaxy include efforts to find bacteria within ticks to stop diseases, as well as an investigation into the incredible nitrogen capturing properties of the fern Azolla. In addition to fostering a growing community of SMRT Sequencing related projects PacBio is also offering a grant program exploring the “most interesting genome” as voted for by the public. 2016 applications for this grant are now closed with a winner to be announced in April.

Science Exchange is also assisting in the Genome Galaxy Initiative with a number of its projects including the Kakapo 125 being managed on its platform. As well as hosting many of the projects Science Exchange is also the easiest and most comprehensive place to find SMRT Sequencing service providers.

science-exchange-smrt-sequencing

The Genome Galaxy Initiative is another great example of the industry coming together to support open access science and to help out with funding at the grassroots level. Science Exchange is excited to be affiliated with this initiative and looks forward to seeing many new and exciting stars being discovered there.

Visit Science Exchange and See Our New Look!

February 25, 2016 | Posted by Team in Company, Helpful products, New Feature, Science Exchange News |

For many people who use Science Exchange, a visit to the homepage is the first step in accomplishing their research objective. For requesters, service providers, or anyone using our network, the web experience is a crucial part of each project. With that in mind, we are excited to announce that we have refreshed the site, including an entirely new homepage. We have kept the same handy tools you will need to start and manage your research project, but improved the look and feel of some key pages. Search our marketplace for thousands of Science Exchange Verified Providers and request a quote in minutes. If your project is more specialized, you can partner with one of our staff scientists to find a perfect fit for your research needs with our concierge service. Every project is covered by the Science Exchange Guarantee, ensuring that your research can begin quickly, safely, and with complete IP protection. Science Exchange is an ideal partner for researchers who want to focus on science instead of sourcing, and progress instead of payment terms. We work with the world’s best suppliers to make scientific discovery faster, easier, and more reproducible. Providing scientists with a single relationship which manages compliance, contracts, and payments allows them to focus on the research goal at hand while collaborating with our cutting-edge providers. We think breakthrough discoveries should happen at the rate of science, not protracted negotiation. Take a look at our ever-growing network to explore how we can help with your next project.Screen Shot 2016-02-25 at 4.34.47 PM

Kakapo 125 – Sequencing the genomes of all known kākāpō

February 1, 2016 | Posted by Team in Science Exchange News |

Kakapo-2

Science Exchange is pleased to announce it will be collaborating in the Kakapo 125 Project. The objective of this project is to sequence the genomes of all 125 known living kākāpō.

The kākāpō is a species of large, flightless, nocturnal, ground-dwelling parrot of the super-family Strigopoidea endemic to New Zealand. It is critically endangered; as of February 2016, the total known population is only 125 living individuals.

The Kākāpō Recovery Team relies on genetic information to manage kākāpō matings in order to ensure maximum genetic diversity. Having the whole genome of all remaining individuals would allow the team to better understand the relatedness of individuals to optimize breeding.

New Zealand Genomics LtdSequencing of the first 40 kākāpō genomes is already underway at Science Exchange’s newest New Zealand based service provider New Zealand Genomics Ltd (NZGL).

The Kakapo 125 Project is the latest project organized by The Genetic Rescue Foundation. The Genetic Rescue Foundation is a not-for-profit organization dedicated to advancing scientific techniques that enable us to preserve global biodiversity. It was founded by Science Exchange software engineer and citizen/wannabe scientist David Iorns.

The Genetic Rescue Foundation has successfully raised funding for the first 40 genomes but is actively fundraising to complete the remaining 85. A core component of this fundraising will be the Experiment.com crowdfunding campaign that will run from February 1st – April 30th 2016. If you would like to help save one of the world’s most unique and charismatic birds as well as playing a part in sequencing the genomes of every individual in an entire species please contribute to the project.

Fund this project

The Kakapo 125 Project is a collaboration between a number of government, nonprofit, iwi and commercial entities.

Kakapo 125 collaborators

All of the collaborators have played an important role in the project to-date. The following individuals have been particularly critical to the projects progression.

  • Andrew Digby, Science Advisor Kakapo/Takahe DOC – Andrew works for the Department of Conservation (DOC) in New Zealand. He is leading the Kakapo 125 Project and conceived the idea of sequencing the genomes of the entire kākāpō species.
  • Bruce Robertson, Molecular Ecologist, Otago University – Bruce’s research focuses on conservation genetics and molecular ecology. He has been working on kākāpō genetics since 1996.
  • Jason Howard, Neuroscientist, Duke University – Jason (in Erich Jarvis’s lab) and his team at Duke were the first to sequence the kākāpō genome.

Sequencing the genomes of all 125 known living kākāpō is an ambitious and exciting endeavor that will help save one of the world’s most endangered species. It will also create a rich, open access genetic dataset that will be the foundation of some compelling research in years to come. Science Exchange is proud to add the Kakapo 125 Project to its long list of impactful scientific projects facilitated and managed via its platform.

Download information about the project in a distributable, media friendly format.
Download press kit


Learn more about how Science Exchange can accelerate your research.

Two Papers Published in the Online Journal PeerJ; First Step to Reproducing Critical Prostate Cancer Findings.

September 22, 2015 | Posted by Keith Osiewicz in Research, Science Exchange News |

Science Exchange published two papers in PeerJ, the online journal, that are being funded by the Prostate Cancer Foundation-Movember Foundation Reproducibility Initiative. This initiative seeks to address growing concerns about reproducibility in scientific research by conducting replications of recent papers in the field of prostate cancer.  It is a collaboration between the Prostate Cancer Foundation, the Movember Initiative, and Science Exchange.  These two papers represent the first step to reproducing the original experiments. Today’s papers are meant to report what the collaborators will do so the scientific community has a full understanding of the process. PeerJ will publish the final results of the replications.

The first paper, The Androgen Receptor Induces a Distinct Transcriptional Program in Castration-Resistant Prostate Cancer in Man by Sharma and colleagues, was originally published in Cancer Cell in 2013. Of thousands of targets for the androgen receptor (AR), the authors elucidated a subset of 16 core genes that were consistently down-regulated with castration and re-emerged with castration resistance. These 16 AR binding sites were distinct from those observed in cells in culture. The authors suggested that cellular context can have dramatic effects on downstream transcriptional regulation of AR binding sites. The present study will attempt to replicate Fig. 7C by comparing gene expression of the 16 core genes identified by Sharma and colleagues in xenograft tumor tissue compared to androgen treated LNCaP cells in vitro.

The second paper Androgen Receptor Splice Variants Determine Taxane Sensitivity in Prostate Cancer by Thadani-Mulero and colleagues was published in Cancer Research in 2014. The experiment that will be replicated is reported in Fig. 6A. Thadani-Mulero and colleagues generated xenografts from two prostate cancer cell lines; LuCaP 86.2, which expresses predominantly the ARv567 splice variant of the androgen receptor (AR), and LuCaP 23.1, which expresses the full length AR as well as the ARv7 variant. Treatment of the tumors with the taxane docetaxel showed that the drug inhibited tumor growth of the LuCaP 86.2 cells but not of the LuCaP 23.1 cells, indicating that expression of splice variants of the AR can affect sensitivity to docetaxel.

Labs listed on Science Exchange will perform the lab work. These labs include Nobel Life Sciences, ProNovus Bioscience LLC, and the Stem Cell and Xenograft Core at the University of Pennsylvania.

UCSC Paleogenomics Lab joins quest for moa genome

August 11, 2015 | Posted by Team in Science Exchange News |

UCSC Logo

Science Exchange is excited to welcome the UCSC Paleogenomics Lab to our platform!

The Paleogenomics Lab is a joint venture between renowned scientists Beth Shapiro, and Richard (Ed) Green. Their research focuses on a wide range of evolutionary and ecological questions, mostly involving the application of genomics techniques to better understand how species and populations evolve through time.

The first Science Exchange project directed to the UCSC Paleogenomics Lab comes from citizen/wannabe scientist and Science Exchange software engineer David Iorns. After a successful Experiment.com crowdfunding campaign David is collaborating with Beth and her team to help perform preliminary sample preparation and analysis. Assuming the samples contain high enough levels of endogenous DNA the prepared libraries will then be sent to collaborator Dr. Guojie Zhang at The Beijing Genomics Institute where the libraries will undergo more rigorous sequencing.

Compiling the genome of an extinct species is an immense challenge. We touched on many of the complexities involved in our original announcement. However the experts participating in the project are world leaders in their field and we are confident significant progress can be made leading to exciting new discoveries about the genetic makeup of this iconic species.

Would you like to collaborate with the UCSC Paleogenomics Lab or any of our other world class laboratories? Learn more about how Science Exchange can accelerate your research.

Sequencing the genome of the extinct moa

June 21, 2015 | Posted by Team in Science Exchange News |

The moa were the tallest birds ever to walk the face of the earth. The two largest species, Dinornis robustus and Dinornis novaezelandiae, reached about 3.6 m (12 ft) in height with neck outstretched, and weighed about 230 kg (510 lb).
Moa

Ka ngaro i te ngaro a te Moa – Lost, like the Moa is lost.

Science Exchange software engineer David Iorns has been fascinated by New Zealand megafauna since childhood. In collaboration with Science Exchange, Experiment.com and the Beijing Genomics Institute he’s undertaking an attempt to sequence the moa genome.

Sequencing the moa genome is a challenging endeavor due the degraded nature of ancient DNA and the large genetic divergence of the moa. Large genetic divergence means the reference genomes required to assemble the target genome are substantially less useful than species with very similar living relatives.

Despite these technical challenges David is optimistic the sequencing attempt will result in the creation of an imperfect yet very useful moa genome. This genome will help to clarify ratite evolution and may even form the foundation of a future attempt at species revival as the science of genetic rescue and de-extinction continues to progress.

The sequencing attempt is being primarily funded via an Experiment.com crowd-sourcing campaign. Please help us to make a meaningful scientific contribution by donating to the project.

All contributions made between Monday 22nd of June 8am PST and Tuesday 23rd of June 8am PST will be matched dollar for dollar by Experiment.com!

Fund this project

OncoSynergy Crowdfunds Ebola Treatment

August 22, 2014 | Posted by Tess Mayall in Science Exchange News |

Can We Defeat EBOLA with an Experimental CANCER Drug? from Experiment on Vimeo.

We are proud to share that Science Exchange user, OncoSynergy, is crowdfunding to test their experimental cancer drug, OS 2966, against ebola infection.

OS2966 is a monoclonal antibody that inhibits CD29 , a main cellular adhesion receptor that is key to cancer progression. Interestingly, CD29  is also thought to be hijacked by the ebola virus during infection. With the current ebola outbreak’s death toll exceeding 1,000 victims, it is more important than ever that promising drugs are investigated as soon as possible. As a result, OncoSynergy is using the Science Exchange network to test whether OS2966 can block ebola infection in cultured human cells.

“We have a unique opportunity to potentially effect a major impact on the current global ebola crisis,” said
Dr. W. Shawn Carbonell, MD, PhD, Founder and CEO of OncoSynergy. “However, as a seed stage
biotech startup with 6 employees, we don’t have the bandwidth to take on projects beyond our central
mission focused on cancer. We are teaming up with Science Exchange and Experiment to accomplish
the initial experiments which are an important first step towards possible clinical testing of OS2966. We
now need the public’s help to fund the work so we can start as soon as possible.”

“I am pleased to be working with Dr. Carbonell on this timely project,” said our CEO, Dr. Elizabeth Iorns. “This is a great example of how the Science Exchange platform can help facilitate science and accelerate scientific discoveries.”

If you’re interested in helping this research progress, please donate to OncoSynergy’s campaign here: https://experiment.com/projects/can-we-defeat-ebola-with-an-experimental-cancer-drug

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