Can Registered Reports help diagnose a reproducibility crisis?

October 14, 2014 | Posted by Reproducibility Project Core Team in Reproducibility |

There has been growing concern in the scientific community over the last several years about a lack of reproducible results in the biomedical research community. Recently, two large pharmaceutical companies (Amgen and Bayer) announced that they could only reproduce a small fraction of published preclinical cancer biology studies. These results have shocked the scientific community, and have lead to calls mandating an overhaul of both funding and publishing practices to address the crisis. The NIH, as well as the journals Nature and Science, are all proposing strategies to help improve the research process.

However, a major question remains: Why weren’t these experiments reproducible? Valid arguments exist suggesting scientists are falling prey to poor experimental design, flawed statistical analysis, and/or biased data interpretation, all of which can prevent their results from being replicable. However, there are many innocuous reasons why a particular experiment might fail to replicate the original results, from errors or changes in the protocol, to a lack of expertise in performing a particular technique, to unknown factors that produce variability in results. Unfortunately, it’s hard to draw conclusions from the Amgen and Bayer studies because these companies made none of their data or methods public.

The birth of the Reproducibility Project: Cancer Biology

We believe that in order to really understand the crisis in reproducibility, including its prevalence, scope and underlying causes, we need a large dataset of actual replication experiments. These replications must be conducted in a rigorously empirical fashion, using detailed protocols as close to the original study as possible, and conducted by expert scientists trained in the original techniques. Most importantly, the details of these replication datasets must be freely available to everyone.

These criteria led us to create the Reproducibility Project: Cancer Biology (RP:CB), a large-scale initiative to systematically replicate key findings from 50 highly impactful recent papers in the field of cancer biology. The project is a partnership between Science Exchange (and our network of expert service providers) and the Center for Open Science, and is funded through a grant from the Arnold Foundation, as well as through donations from many generous vendors. The goal of the project is to clarify the variety of challenges that exist for reproducibility, and encourage discussion of data-driven solutions from researchers themselves, as well as for policy makers at funding, publishing, and government institutions. To that end, all our findings will be published by the open-access journal eLife. Additionally, all of the methods, data, and results of the replication studies to be available for anyone to review on the Open Science Framework. Read the rest of this entry »

Find relevant scientific articles quicker

October 8, 2014 | Posted by Tess Mayall in Helpful products |

Sparrho imageWhen I was in grad school, I was expected to track and know every new piece of research that related to Indian Monsoons. However, no one told me how to do that. I didn’t have the years of experience and I definitely didn’t have the time to sort through the endless new articles coming out on a regular basis. There is now a website called Sparrho that simplifies the overwhelming process of tracking scientific articles.

Sparrho compiles scientific sources to one place and brings the latest and most relevant scientific news (including papers, grants, and patents) to users. Most importantly, Sparrho learns. As you continue to use Sparrho, it will learn your preferences and needs so that you can spend more time reading relevant articles, rather than digging for them. Read the rest of this entry »

Science Exchange Stories: Ethan Perlstein, Perlstein Lab

September 25, 2014 | Posted by Tess Mayall in Scientist Spotlight, Stories |

Perlstein Lab Cropped

I recently spoke with our user Ethan Perlstein, whose one-of-a-kind independent lab is flipping traditional drug discovery on its head. Check out how he is changing the paradigm of traditional research, pharmacology, and more below.

Q: What is the focus of the Perlstein Lab?

Ethan: The Perlstein Lab is focused on personalized orphan drug discovery. We take a two-pronged approach. We first create a primordial disease model for a given patients’ mutation; that involves taking a change in the DNA that you see in the disease and putting it into the model organisms.

We use yeast, worms, flies, and fish that have ancestral versions of that gene. We can use those models to do drug discovery, and we can validate the hits that we get in patient derived cells of the same genotype. So it’s a closed system where everything is personalized from the outset.

Q: How did it come into existence? What was the progression from your very first crowdfunding experience to starting your own lab?

Ethan: The science behind it has been incubating a long time, since I was in grad school, so it’s been a ten-year process. Screening using a model organism is something I did in grad school, so it’s existed for awhile. As a post-doc, I took some of those scientific concepts and drilled down deeper, so that put me in a good position to have a scientific foundation.

I spent the next 18 months leaving academia and navigating the business side. Last fall, I put together a business plan, had it reviewed by business people, improved my plan, and by the end of 2014 I began fundraising.

The team started to come together in early April. The lab started to come together in terms of equipment and structure in mid-April. And now we have a fully functional lab that has yeast, worms, and flies, and it’s off to the races. Read the rest of this entry »

eLife will publish Reproducibility Project: Cancer Biology results

August 28, 2014 | Posted by Elizabeth in Reproducibility |

We are excited to announce that eLife has joined our partnership with the Center for Open Science to work on the Reproducibility Project: Cancer Biology!

eLife is an open access journal co-founded by the Howard Hughes Medical Institute, the Wellcome Trust and the Max Plank Institute. We are proud to have the work of the RP:CB published through them.

Each study in the RP:CB will undergo two rounds of review and publication. The first round will present the proposed replication plan to the public in the form of a Registered Report. This Registered Report will ensure that the proposed protocols have been reviewed by scientific and statistical experts prior to experimental work commencing. The completed work and all data will then be published as a Replication study. All data generated will be freely available to the public through eLife’s open access platform. Registered Reports are now under review by the eLife Board of reviewing editors and will be published in the eLife journal as available.

The Reproducibility Project: Cancer Biology aims to replicate key findings from 50 high profile papers from the field of cancer biology.

“We need an objective way to evaluate reproducibility,” said Randy Scheckman, who is the Editor-in-Chief of eLife and a Nobel prize winning cell biologist at the University of California- Berkeley. “This project is a valuable opportunity to generate a high-quality dataset to address questions about reproducibility constructively and rigorously.”

For more information, please see eLife (http://elifesciences.org/eLife-the-Center-for-Open-Science-and-Science-Exchange-partner-to-assess-the-reproducibility-of-cancer-biology-research) and the Reproducibility Project: Cancer Biology (http://validation.scienceexchange.com/#/cancer-biology). Read the rest of this entry »

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

New Feature: Lab-Initiated Quotes (LIQs)

July 29, 2014 | Posted by Brianne Villano in Lab Admin Tools, New Feature |

Just a few weeks ago, we introduced you to our new quotes with line items. There has already been another exciting development for the site and we want to share that with you as well!

Lab-Initiated Quotes, or LIQs (“licks”) as we affectionately call them, are a way for any lab to begin their interaction with a researcher by sending a quote directly to them, whether they are already on Science Exchange or not. Some terrific applications for LIQs are in cases when you’ve been discussing the scope of work with a researcher over email or the phone and want to send them a quick quote so they can accept and get the ball rolling on the project as soon as possible. Read the rest of this entry »

Lab Profile: Ben Woodard, Director, Biotech Research and Education Program

July 16, 2014 | Posted by Tess Mayall in Lab Profiles |
Ben Woodard (right) Director of the Biotech Research and Education Program.

Ben Woodard (right) Director of the Biotech Research and Education Program.

I recently spoke with Ben Woodard, Director of the Bioprocess Scale-Up Facility on Science Exchange. They help take research to the next level, literally. They scale up existing scientific procedures to make them ready for commercial production. Check out more on their interesting and unique niche below!

Q: What is your role with BREP?

Ben: I’m the Director of the Biotechnology Research and Education program (BREP) at the University of Maryland. The program encompasses two core facilities including the Bioprocess Scale-Up Facility that focuses on yeast and bacteria processes and the Biopharmaceuticals Advancement Facility that focuses on adherent or suspension-adapted cell lines such as HEK293, CHO, Sf9, NSO, and MSCs.

Q: How did the Program come into existence?

Ben: The program began with just the Scale-Up Facility. In 1985 the University and my department, then The Engineering Research Center, felt that there was a need for a laboratory that would enable collaborative research between academics and industry.

The faculty had great ideas, but they didn’t know how to commercialize them, they didn’t know how to take a product to market. The industry had challenges with their processes that needed the expertise of the academics. So the Facility was created to link these two groups together. When it began in ‘85 it was one of the only contract research facilities on the East Coast, it was pretty novel at the time.

We were created to spark economic development for the State while providing small start-ups, faculty researchers, and student researchers with a knowledge base that would help them create novel and new technologies. Ultimately trying foster growth in the Maryland biotech sector.

Q: What are the most popular experiments?

Ben: Cell culture and fermentation projects, protein expression and purification. We specialize in taking a cell line that’s been modified and scaling up its production for pre-clinical research. Additionally, we have fantastic training and workforce development program that has trained over 200 technicians and researchers for the biotech industry.

Q: What are some of the major projects you worked on?

Ben: A major success was a product called Synagis, a top selling biopharmaceutical. It’s used to treat respiratory syncytial virus, a virus that prevents proper lung development in premature babies.

A second major project was our work with Martek and their product LifesDHA.  It’s a fatty acid that’s been linked to brain and eye development in children.  DHA is naturally found in breast milk, but Martek, with the help of our facility, was able to optimize its production in algae. Just about every child in North America under the age of 14 has consumed their product.

Our service isn’t to identify proteins or antibodies such as these, it’s to provide research, optimization, scale-up, and the like, to support the efforts of the biotech community.  We provide services that are crucial to the long term growth of a biotech product.

A parallel would be if you make a Duncan Heinz cake for your office. You get an egg, you mix it up with the mix and a little oil, bake it and you can feed 5 or 6 people. Now make that cake and feed the entire Northern hemisphere. Do you add 1 million times more eggs? Bake at a different temperature? You can’t just multiply the number of eggs by the anticipated number of servings. You have to change variables such as temperature, the size of the pan, and the ratio of oil to mix, in order for the cake to bake correctly.

Now for us, a researcher or clinician may have an idea that they’ve researched in small scale and found they can produce a small amount, a few milligrams  of a protein or antibody, perhaps enough to treat a mouse.  Now how do you scale-up that product to treat 4 or 5 million people? That’s where we come in.

Our mission is three-fold: do contract service work, help workforce development, and support education and research opportunities for undergraduate students.

Q: How did you end up working there?

Ben: I started as an undergraduate student in 1994 in the fermentation facility. I was working on workforce development project for MedImmune, training over 100 of their employees, and I really enjoyed the work in and the interaction with other.  I’ve been involved with the BREP since.

Q: How has your experience been using Science Exchange?

Ben: It’s been great. It’s been a unique opportunity to expand our reach outside Maryland. Being a state university we don’t spend a lot of money on marketing, but with Science Exchange we can utilize equipment that’s normally stagnant. Science Exchange allows researchers from other institutions to access equipment that would’ve been idle. Working with Science Exchange has really been a great source of opportunities for us to make our equipment operate at a higher volume.

Check out more on the Bioprocess Scale-Up Facility at their Science Exchange storefront.

About the author

Tess Mayall builds Science Exchange’s online and offline community of scientists and providers. She is a geologist by training, but considers herself a friend of scientists near and far.

 

 

New Feature: Line Items for Quotes

July 8, 2014 | Posted by Brianne Villano in Lab Admin Tools, New Feature |

This has been an incredible year for Science Exchange. Our team has grown and our site is continually improving based on feedback we receive every day from researchers and lab admins alike.

Our newest feature was one of the most commonly requested from the lab admins on our site. It began as a discussion with the Lab Advisory Board – the LAB for short.

Previously, lab admins were able to submit text in a large description box, upload any pertinent files (like their institution quotes that included line items), and a price for the project. So in order to make the quoting process more flexible and intuitive, we’ve built line items into our existing quote system.

Labs are now able to generate their own line items within Science Exchange!

New line items for quotes

Read the rest of this entry »

Science Exchange Stories: Derek Duan, Eyegenix, LLC.

June 26, 2014 | Posted by Tess Mayall in Scientist Spotlight |
BioSynthetic Artificial Cornea of Eyegenix LLC.

BioSynthetic Artificial Cornea of Eyegenix LLC.

Derek Duan is a Principal Investigator at Eyegenix, a small biotech in Hawaii that is creating a unique way to cure corneal blindness.

How are they doing it? By creating a synthetic, transplantable cornea that promotes tissue regeneration.

I spoke with Derek about their novel approach to curing blindness, the biotech scene in Hawaii, and his experience using Science Exchange. Check out our conversation below.

Q: Tell me about Eyegenix.

Derek: We’re a biotech company located in Honolulu, Hawaii. We’re doing research and development on the most advanced artificial cornea in the world. This is a biosynthetic polymer based product.

We’re very excited to put our artificial corneas into the market as soon as possible, because there are millions of people globally that could be cured with this product.

Q: How did the company start?

Derek: Dr. Hank C.K. Wuh, who was born in Hawaii and educated in the mainland, founded the company in 2012. He wanted to come back and serve Hawaii. He’s making use of the island as an intersection of Asia, Australia and America to be a center for biotech research. That’s why he decided to come back and fund his company. Read the rest of this entry »

Lab Profile: Zhiyong Wang, ADS Biosystems

June 19, 2014 | Posted by Tess Mayall in Lab Profiles |

 

Zhiyong Wang in the lab at ADS Biosystems.

Zhiyong Wang in the lab at ADS Biosystems.

I recently talked with Zhiyong Wang Ph.D, CEO of ADS Biosystems Inc. ADS Biosystems specializes in cell-based assay development. In particular, Zhiyong applies his experience and expertise from the renowned Hunter Lab at the Salk Institute to develop assays with brown and white fat, routine human cell lines,  human adult stem cells, and rodent cochlea.

Check out more on his background and inspiration below.

Q: What were you doing before you started ADS Biosystems?

Zhiyong: From 2002 – 2009, I was a research associate in the Hunter Lab at the Salk Institute. The lab is fantastic and everyone enjoys developing and working on their own projects. It’s a great environment with diverse expertise and collaborative spirits. Tony encourages people to be independent and explore what inspires them. Tony co-founded the Signal Pharmaceutical Inc., which is now part of Celgene Corp. Therefore, it is not surprising that a few people from his lab have started their own companies.

I was researching metabolism, obesity, and diabetics with mouse genetic models, and discovered crucial roles of transcriptional master regulators in obesity and glucose resistance. I was fascinated with fat cells (adipocytes) in particular.

That was the reason why I was recruited to a local stem cell company that planned to build a brown fat program from scratch. At that time, there were exciting discoveries that adult humans have brown fat, which burns energy and may be used to combat obesity and diabetes. I was really excited about the project and enjoyed building the brown fat program from the ground up. I discovered a family of small molecule compounds that induced brown fat formation from human adult stem cells. I also developed a platform to discover novels compounds, which induce brown fat formation in obese patients to burn extra energy.

Another project at my previous company started with a Department of Defense (DOD) grant. As you know, some of our soldiers at Afghanistan and Iraq experienced battlefield noises and lost their hearing. We wanted to restore their hearing by stimulating stem cells in cochlea to regenerate inner ear hair cells, which are responsible for sound wave sensing. As the lead scientist for the project, I developed cochlear organ culture-based assays to identify candidate compounds, which induce hair cell regeneration. Our hearing team was great in that we really enjoyed working together and we were very productive: we generated two patents for the compounds of hearing restoration and discovered a novel pathway critical for inner ear hair cell regeneration. Read the rest of this entry »

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