It’s no secret that here at the Depot, we love CouchDB. We have been using CouchDB as our main database for a couple of years now. In that time, the team responsible for creating couch has formed a company, Couch.io, to foster and support the growing community. Couch.io recently did a case study on the way Assay Depot uses Couch. If you are interested in a taking a peek under the hood of how Assay Depot works (or want to get more familiar with Couch) head over there now and take a look.

CouchDB is really taking off. I was excited this week when I got a note from Andrew Su at the GNF informing me that BioGPS has converted to CouchDB. If you’re not familiar with BioGPS, it’s a great resource for learning about gene and protein function. It’s a great product; if you are looking for information about genes or proteins, I’d recommend checking it out.

Just last week we release our faceted browsing feature. This week we are following it up by adding the entire contents of our internal database of suppliers to the website. Our database is the most highly curated database of pre-clinical CROs anywhere consisting of more than 2,300 vendors, with more added everyday.

You can access this database right from our homepage:

There is a link to view all providers right on our homepage

If you know the name of the CRO you are looking for, you can browse an alphabetical list:

Browse CROs by name

Or you can search for any term you like and look for providers that way (try searching for proteomics or next generation sequencing):

Searching for Next Generation Sequencing returns over 70 CROs

Finally, you can still narrow your search by certification or location. We hope you like the new feature, please add a comment if you have any ideas, concerns or suggestions. Happy searching!

We’ve been hard at work here at the Depot making the site more user friendly. If you use our site often, you’ve probably noticed some changes to our search interface. First of all, I hope you’ll try the new faceted browsing. If you’re not familiar with what faceted browsing is, think of when you shop for a digital camera. You can browse by brand (Canon vs Nikon), you can browse by Megapixels (8 vs 10), you can say you’re only interested in DSLRs or any combination there of. Well now you can search for Research Services or CROs the same way. The following are some of the results you get when searching for “protein” on assaydepot.com (click here to try it):

Results when searching Assay Depot for protein

You can see some of the “facets” that are available. You can search for protein services, but then narrow to only services offered by CROs that are ISO9001 certified or that are located in Canada… or both!

We’ve also added the ability to search for CROs. Assay Depot is and always will be service based. Meaning, we want to give you the service you are looking for, not just the name of a CRO that might offer it. However, people still want to know who’s out there, so we’ve added the ability to search for CROs directly (click here to try searching for providers):

Search Assay Depot for providers

I hope these upgrades help you find the services you need. We’ve got some more search upgrades in the works, so check back soon!

We began this blog to start a discussion about new models for drug discovery, and we’re trying to engage you and other bloggers to participate in the discussion. We thought it would be helpful for us to provide some links and shortcuts for you to help you keep in touch with drug discovery blogs and news.

Most of the blogs below have a blogroll to help you find other sources, and we encourage you to learn about using RSS feeds to get information whenever they are updated (learn more about RSS feeds and readers here). To get you started, here are some shortcuts.

Do you have a source you’d like to share? Leave it below, and we also encourage you to interact with us and the bloggers we’ve listed, as it moves us towards our goal of revolutionizing the drug discovery process.

Have you taken a test drive of the Assay Depot marketplace yet? Signing up is easy, and you can even look around without signing up, so by all means go for it. If you’re the type that likes to kick the tires, though, here is a short tour of how we’ve set things up to help you find what you’re looking for. Also, you might even learn something new about the assays utilized in drug discovery and development.

To begin with, we’ve categorized our services by the functional units typically found in drug discovery organizations, namely biology, chemistry, dmpk, pharmacology, and toxicology. Each discipline is in turn broken out into subdisciplines, which list assay categories. Clicking on the category will list all of the assays for the category.

Why is this expert categorization important? Searching is great, but browsing is important, too. Seeing the assays in context, and also related assays, helps you to choose and plan. While browsing, even if you aren’t logged in, you’ll be able to see the details of each service, including sample type, turnaround time, and the results you’ll receive. By clicking on the ‘Add to Cart’ button, you’ll be able to download a spreadsheet which gives you much more information about the samples and information you will need to provide. You can also ask questions directly to the service provider by clicking on the ‘Request Info’ button.

Prices are listed, to help you budget, unless pricing requires more information. In this case, click on the ‘Request a Quote’ button, and you can even request a quote from more than one service provider. We also provide related services at the bottom of each service listing, and these results are curated by our drug discovery experts. In addition, you may want to look at other categories or subcategories to plan your experiments accordingly. This feature is one of the benefits of the organization of the marketplace.

We’ve also put a lot of thought into the search feature. Using the search input at the top right, you can enter the name of a service or key word, and the results will appear in the main window. Every service provider with a service that matches the search term is listed on the left, and you can click on any of them to see all services provided. In the main part of the window, the services are listed. Those that require a quote will have a ‘dialog’ icon in the top left, others will have a ‘test tube’ icon. You may also notice that the color coding for each service is based on the discipline it’s in, so you’ll always be able to orient yourself.

We think that our detailed characterization of the Assay Depot marketplace services will help you not only find the service you need quickly, but may also help you to learn about other assays that you may not be as familiar with. We think that besides the benefit of being able to search and compare services, that a more comprehensive understanding of assays used in drug discovery will help researchers to accomplish more. We’re open to your feedback, please leave any comments below.

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I attended the Society for Biomolecular Sciences Label-Free Symposium in San Diego last week. The area seems to be growing quickly, as it utilizes diverse technologies to facilitate more biologically relevant biochemical and cell-based assays. The benefits include shorter assay development time, less interference from labeling or non-native cells, the ability to study live cells, and access to kinetic data. Additionally, the technologies can be used for applications such as fragment-based drug discovery and for analyzing protein-protein interactions.

Some of the take home messages from the symposium centered around the fact that more comprehensive, biologically relevant information can be collected more easily with label-free technologies. Some talks pointed out that the information can be less ‘binary’ than the hit/no hit answers we’re used to getting from high throughput screening (HTS), meaning that more information can be gleaned, but that more sophisticated data analyses may be needed. Although the conference appeared to feature a whirlwind of technologies, from calorimetry to optical biosensors to mass spectrometry, the same targets kept re-emerging (GPCRs, 7TMs). Thus, there is a common theme to these tools: they give us information that was difficult to obtain before.

How do the technologies work? There is no single answer, because they are so diverse, but basically they measure molecules interacting or cellular phenomena by detecting perturbations in the system. For example, optical biosensors used with surface plasmon resonance (SPR) detect a change in the refractive index when a protein binds a small molecule or protein, for biochemical/protein assays. For some label-free cell-based assays, a change in impedance is used to detect changes in cell morphology, adhesion, or viability. Check out this presentation from Corning (PDF) which shows how their Epic^© System works and can discern between different GPCRs and types of effectors.

Many of the talks at the SBS symposium were from drug discovery scientists from pharma/biotech, and each speaker usually focused on a particular instrument. At first, this made the conference feel as if it was too ’sponsored,’ but I think it might just be the nature of the industry, as most have a ‘favorite’ instrument. Here is a table outlining the companies/instruments that appeared to ’shine’ at the conference. Interestingly, Biacore/GE Healthcare did not exhibit or present at the conference, although their instruments have been a mainstay in SPR.

What is the drug discovery 2.0 connection with label-free technologies? Reports on both  cell-based and biochemical label-free technologies predict a significant impact for drug discovery (links are to summaries–full reports must be purchased). A Drug Discovery World summary of the cell-based report detailed that the most impacted areas are likely to be hit identification and lead optimization. Some nice reviews exist in the literature, as well as this freely available one I found. Label-free technologies have the potential to streamline and standardize assay development for different targets and also provide an orthogonal, rich source of information that complements existing methods. Improvements in throughput, for example as seen with the Fujifilm AP-3000 instrument for SPR, mean that larger numbers of correlations are now possible.

Does the Assay Depot marketplace offer label-free assay services? We’re not aware that any of our providers specialize in these types of assays, but we spoke to several companies at the conference and got a great response. Stay tuned!

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How do service providers benefit by being a part of the Assay Depot marketplace? Besides having access to the desktops of pharma, biotech and academic researchers and managers around the world, you’ll find many benefits to joining. Drug discovery researchers are busy, and searching for providers is time consuming and inefficient.  Online contract research organization (CRO) directories tend to list just the basics, leaving customers with a lot of follow up work. Assay Depot makes the decision process much easier and faster, increasing the likelihood of obtaining business. We provide a detailed listing of your services and guide customers through the search and selection. We also streamline the legal process, which we all know can be costly and time consuming.

Listing your services with Assay Depot is easy. We’ve created a simple interface for you to enter and update your service listings.  You might even find that it helps you organize your offerings internally. You’ll be able to log into a single interface and manage all of your quotes and projects … for all of your Assay Depot clients. We think that will save you time and money.

We’ve actually saved the best for last in this post. An important part of negotiating and implementing a successful service project is communication, and we’re betting that you spend a lot of your resources on this function. We’ve built a unique, sophisticated, and intuitive interface for you to discuss every aspect of your services and projects with clients. In many ways, we’ve created ready-made customer relationship management (CRM) software specific to each service that your business offers.  More on this private microblog concept later.

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How have you been finding and evaluating pre-clinical contract research organizations (CROs) for your drug discovery programs, and how straightforward has it been to utilize them? The answers probably vary widely among researchers and managers, and even between the different types of services you’re outsourcing. Many directories of providers exist – what makes Assay Depot different?

Most provider directories are a collection of data about CROs. Which is nice, but most of the ‘pain’ of outsourcing comes from what comes next: the information exchange, the negotiations, material transfer, and project milestones and deliverables. Assay Depot’s marketplace provides you with this information, and also detailed, actionable listings for more than 2000 assays and services.

So, you won’t be left with just a phone number from a directory, you’ll be able to research, compare, and execute services. We make it easy by taking care of the legal process, allowing you to communicate regularly with the providers, and helping to manage your data and materials. We’ll be starting a ‘howto’ series soon, and signing up is very easy, take a test drive!

You’ll benefit both in the short and long term by using Assay Depot. In the short term, your projects will run more efficiently, accelerating research and encouraging innovation. Long term advantages include capturing metrics which enable procurement cost-reduction strategies and improve outsourcing oversight. Consolidating and optimizing the outsourcing workflow frees up resources in legal, finance, and administration.

Want the really big picture? By standardizing the services, and providing head-to-head competition, improvements in quality and overall value will result. It’s a win-win situation for customers and CRO providers. Utilization of CROs is growing at a compound annual rate of 16%, and is expected to reach $8B in 2013 (Kalorama Outsourcing in Drug Discovery, May 2008). A survey of drug discovery researchers and managers indicated that 41% planned to increase outsourcing by 10% or more in 2009 compared to 2008 (Contract Pharma 2008 Outsourcing Survey).

We think it’s a great time for you to take advantage of new efficiencies made possible by the Assay Depot marketplace. We’re looking forward to sharing our experiences with you and discussing the future of drug discovery.

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Assay Depot was founded in 2007 by a software developer (Chris Petersen), a chemist (Andy Martin) and a cell biologist (me).  The three of us had worked together at a drug discovery company in the early 2000s and had discovered firsthand how difficult and heart-breaking drug research can be.  We joined together again to found Assay Depot because we saw an opportunity to build a company that could significantly improve how drug research is done.

By 2007, research outsourcing had already become an important component of pharmaceutical drug discovery.  Pharmaceutical researchers (who spend the bulk of drug research dollars) were increasingly purchasing research services from external service providers (aka Contract Research Organizations or CROs), and the number of CROs had skyrocketed from just a handful in the early 1990s to many thousands located throughout the world.  Yet, despite the huge increase in the number of research customers and CROs, there was no systematic way to find, compare and order outsourced research services.  Each CRO needed to be approached individually, often by phone.  Non-disclosure agreements, master services agreements (MSAs) and prices needed to be negotiated.  Billing and data reporting processes needed to be set up.  It could and did take months before the actual research service was initiated.  To make things worse, this entire unwieldy process needed to be repeated every time a researcher needed a new service.

We recognized that simply creating an online database of CROs would not address the core inefficiencies of outsourcing.  To make the process more efficient, we would need to build a comprehensive provider database and do at least five additional things:

1. Provide highly detailed scientific information about the services for sale;
2. Make service pricing much more transparent;
3. Shorten the time-consuming and expensive legal process;
4. Establish a direct communication link between the CRO and researcher; and
5. Enable CROs to respond to quote requests and manage their orders online.

We spent most of 2008 creating an online marketplace (located at assaydepot.com) that satisfies these five requirements.  On one website, researchers can now find and compare highly detailed scientific information about thousands of research services.  They can place orders for these services without having to negotiate prices, as many CROs list service prices on the marketplace.  Likewise, they can place online orders on the marketplace without having to negotiate any legal agreements, as all CROs have pre-signed a standard MSA covering confidentiality and service performance.  They can also use Assay Depot’s online quote request forms to simplify the design of custom services and, before and after ordering a service, they can communicate with CROs through a private microblog.  The net result for the researcher is that outsourcing becomes easy.  Thousands of research services are now at their fingertips, ordered in just a few mouse clicks.

The benefits for the CRO are significant as well.  For them, the marketplace is a single Amazon-like store where they can create and list services, respond to quote requests, communicate with researchers and process orders.  They promote their own brands but since Assay Depot helps finds the customer, pre-establishes the MSA and also carries out the billing/invoicing for the service, they can offer services with only limited internal administrative support.   Their primary focus can be on creating quality services that researchers need.

Can an online outsourcing marketplace really change how pharmaceutical drug discovery is done?  That won’t be easy, but in theory at least the concept is simple.  Once the marketplace reaches a critical mass of service providers, drug researchers will be able to access any service they need, the moment they need it.  For the first time in the industry’s history, a single scientist will be able to run an entire drug discovery program (cost-effectively by today’s standards) from a laptop computer, without doing any laboratory work whatever.   I think that capability could be game changing.

I will expand on what I think that means for the industry in future posts.  For now, though, I want to make it clear that by improving the outsourcing process we are not to trying to replace pharmaceutical scientists.  Our goal is the exact opposite – to remove the routine from research so that scientists can focus on the innovative research that will really make a difference in their lives and ours.

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