Pharm2Market – Connecting The Life Science Community

Starting a biotech company is challenging at the best of times. In her book “How To Start A Life Science Company”, Dr Leah Cannon describes some of the business challenges that biotech companies face: the attrition rates for drugs remain high, the regulatory requirements are continuing to grow, and finding the right investors and partners continues to be challenging.

One of the biggest success factors for biotech companies; however, is the ability to leverage your local community to find the resources you need to advance your drug discovery programs. And after months of conversations with local biotech companies, we’ve built a new web app called Pharm2Market to help connect people in life science communities.

In this article we’ll take a look at two-sides of the networking table:

  • the founder/innovator responsible for bringing that new medicine to the table;
  • the business development professional, responsible for providing a product or service in support of a drug discovery program.

Pharm2Market started as part of our own internal business development effort. We found ourselves collecting a wide variety of information on potential customers in the communities we serve — San Diego, San Francisco, and Boston. Everything from basic business information like address and contact information to funding and pipeline information.

Pharm2Market represents a different approach to helping customers connect the dots — by helping them identify the resources, investors, networking opportunities, and news that helps drive their business. Pharm2Market is business intelligence for biotech communities.

What Can Pharm2Market Do For Founders?
Let’s say you’re the founder of a drug discovery company, you can use the Pharm2Market to identify investors by comparing your company to similar companies, and looking at their funding sources.

We also help you find the resources you need to advance your drug discovery programs. Everything from finding legal advice on company formation and IP, to finding lab space, lab instrumentation and reagents.

Pharm2Market connects you with professional societies to help expand your network and keep track of all the local networking opportunities.

Pharm2Market keeps you up-to-date on the latest news in your community, industry and field of study by providing news from sources like the San Diego Union-Tribune, Xconomy – San Diego, FierceBiotech, Genome Web, STAT, Genetic Engineering News, Drug Discovery News, New Scientist, In The Pipeline, wire news services and much more. The Portfolio feature allows you to track the news on a specific set of companies.

What Can Pharm2Market Do For Business Development Professionals?
If you’re a business development professional, Pharm2Market contains information on over 200 local San Diego drug discovery companies. We track the projects, targets, therapeutic areas and therapeutic classes, pathways, and clinical trials that companies are involved in. This makes it easier for you to identify potential business opportunities, and helps insure that when you walk into a meeting with your next customer, you do so with a better understanding of their business.

If your company provides lab space, construction or facilities services, you can use Pharm2Market to identify companies in need of expanded lab space, or lab remodels. If you provide contract research or manufacturing services, Pharm2Market can help you identify customers with Phase 2 and 3 projects who need your services in order to complete their clinical trials.

Pharm2Market helps you keep track of news and tweets of companies in your communities.

Concierge Services
Sometimes it’s not enough to simply provide people with access to a database and hope they’ll be able to connect. You have to take the time to understand their business and help them connect. To help make that happen, we’re launching a concierge service. We will work with you to define the target market you’re trying to address, and then do the detective work for you to help you connect with the right people.

The Road Ahead
Pharm2Market is a very community-focused application. We’re launching with support for the San Diego community first, followed by San Francisco in the January, and Boston in Q1 of next year.

We’re also looking at ways to use Google’s machine learning service (known as “ML Kit”) to help identify new potential partners for our customers. You can think of it as for drug discovery communities.

Our initial packages were designed to help founders and business development professionals connect with one another. As we’ve been building out Pharm2Market though we’ve had a few inquiries from individual scientists wanting to connect local companies. We’ve been thinking about creating a package specifically for them — with news, company profiles and job search features. If you’re interested in helping us think through the feature set, you can reach out to me at one of the SDEE Happy Hours or connect with me.

How can I get started with Pharm2Market?
You can sign up for an account at

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San Diego Biotech Networking Tips

People network for two basic reasons: to expand the pool of potential job opportunities, and to find sales/partnering opportunities. In this post, we’ll take a look at some of the common career networking mistakes, tips for getting the most out of networking events, and career networking resources available to biotech professionals in San Diego.

Common career networking mistakes
The most common mistake that people make is to treat networking as a chore that you do when you’ve lost your job, or your company has imploded. In reality though, networking is one of those critical skills that is an integral part of managing your career. Moreover, networking can help you understand the good and the bad about the companies in your community. You’d be surprised at what you’ll learn over a beer.

But beyond simply identifying your next position, networking is a invaluable way of learning from others in your profession, and learning how to take the next steps in your career. It can help you find that mentor that point you in the right direction and keep your career from stalling.

Failing to budget enough time for networking is another common mistake. You’re busy managing the job you have, and not really thinking about the next step in your career. Your weekends are filled with hobbies and family commitments, and networking is often one of those activities that just falls off the list.

Budget one day a month for networking, and treat the process like a game not a chore. Identify the types of people you want to connect with, and use LinkedIn to keep “score” of the numbers of new connections that you’re making at the events.

Don’t use LinkedIn as a surrogate for face-to-face networking. It’s easy to simply reach out and connect, but unless you’re actively engaging with them, you’re not getting any real value out of the relationship. Moreover, if you’re connecting with everyone and their grandmother, the recommendations that LinkedIn gives you for potential new connections will be diluted to the point that they cease to have any value for you.

Tips for Improving Your Network
Here are a few tips to improve your network:

  • Do your homework – before the event, take a look at the attendee profiles for the people who have RSVP’d. Most of the networking groups use either their own networking software or Eventbrite or to manage the event, and each of these platforms let you view the profiles of the event attendees. In some cases, the software will let members attach their LinkedIn profiles to their Eventbrite or Meetup profile and this makes it easier to research potential new connections. Make sure that you include your LinkedIn URL in your profile. Identify what type of person you want to connect with, and review the attendees to identify the ones that fit that profile.
  • RSVP Early – with some events, your chances of connecting with your target audience will improve simply by RSVPing early to the event. The reason for this is that as people checkout who’s coming to the event, they’ll see your profile and decide that they want to attend as well. I’ve noticed the attendee list for some events will snowball in the last two weeks before an event, so make sure that you check the event site multiple times.
  • Bring business cards – I know it’s old fashioned, but it works. People are more likely to connect with you if your card says something about you. A big mistake that I often see with people is using some cheap service to create business cards that look cheap. They often only have the person’s name and their personal email address. Take a look at a printing service like Moo. Add a graphic to your card to make it stand out. Use a professional looking email address for professional interactions – something like “” says the wrong thing about you. Put some keywords on the back of your business card that say what kinds of skills you bring to the table. Make sure that you add your Twitter handle, blog (if you have one) and your LinkedIn profile link. If you use Facebook for professional networking, make sure that you include it as well. But also make sure that you segregate your Facebook connections into professional and personal groups.
  • Bring a notepad – bring something to scribble notes on or use Google Keep
  • Create an elevator pitch – this is a short verbal statement of who you are, what you do and what you bring to the table. It helps to write it down and practice it. Remember to keep it short, and keep it memorable. You might start by crafting a personal mission statement, and then elaborate on it a little bit. You want it to be short enough that you can memorise it, and long enough to be interesting. If you run out of ideas, look at your LinkedIn summary and see what you can borrow from that.
  • Use the LinkedIn app – Occasionally, despite your best-laid plans, you’ll run out of cards at an event. If you’re lucky the other person also has the LinkedIn app installed on their phone. Here’s a neat trick to pass along to everyone you meet at the event, ask them to open LinkedIn, tap the My Network icon at the bottom of the screen, and tap the Find nearby (OFF) icon at the top of the screen. This turns on a hidden little feature in LinkedIn, like a personal radar, that says “I’m here, connect with me”. It also lets you see who else at this location has their radar turned on. The names of the people nearby appear at the bottom of the screen, and you can tap their profile cards to request to connect with them.

Networking Resources
Here are some local groups that can help you get started:

AWIS San Diego – the American Women In Science meetup group is a great way to connect with other scientists and entrepreneurs in the San Diego area — no, you don’t have to be a woman to attend.

Biotech Beach Brewery Meetup – is another local meetup group for biotech, pharma, and healthcare professionals.

Connect – connect is an organisation that brings together entrepreneurs in the various tech & biotech communities in San Diego, with investors and resources that they need to succeed. The connect meetup group can help you identify potential investors.

San Diego Pharmaceutical Project & Portfolio Management Meetup – this group is dedicated to helping pharmaceutical project and portfolio managers network and learn from one another.

SDBN – San Diego Biotechnology Network is one of the most popular networking groups in San Diego. It was started by local biotech marketing maven Mary Canady, and remains a fixture of the San Diego Biotech scene. They host speed networking and other events. The next one is scheduled for August 1

SDEE – San Diego Entrepreneur Exchange is a great resource for connecting with other biotech entrepreneurs in the San Diego area. They host a monthly Happy Hour at New English Brewing. If you have an idea for a biotech startup, want to work for one, or want to partner with one, this is the place to meet. The next one is scheduled for August 16

Suds & Science – Suds & Science is a networking group that combines both a networking event and a learning experience. They meet at breweries in San Diego, and you connect with other professionals and learning something new and science-related.

Posted in biotech, networking, Pharmaceutical, Social Media | Tagged , | Leave a comment

Build, Buy or Both

Over the years, we’ve been involved in a number of LIMS/ELN selection projects. In this new series of blog posts, we’ll take a look at some of the lessons learned from those projects.

There are a variety of circumstances that can drive the decision to build or buy a system. Here are a few questions that you can use to help you better understand where you might fit on the spectrum.


  • Do we have the internal resources, processes, experience and technology to build the application ourselves?
  • Can we outsource this effort? Can we do this with the proper oversight necessary to see this to its conclusion?
  • What is the opportunity cost involved in dedicating internal resources to this effort? If I’ve tied up my informatics department in these software engineering tasks, will it prevent them from addressing these higher value needs that my scientific groups have?
  • What are the ongoing costs going to be to maintain this system?
  • Could we open source the parts of the system that aren’t proprietary? Would that alleviate some of the maintenance burden on the staff? Is there a community of practice that this would benefit and that would be able to share some of the costs? Organizations like the Pistoia Alliance which focus on implementing pre-competitive technologies and standards might be a way forward.


  • Does the solution address most of our business processes? If not, can multiple solutions be integrated into a seamless whole?
    • What is the cost of integration?
    • What will the maintenance cost be for each of these integrations? Each time a vendor updates an application, the integrations between that application and other applications will have to be re-tested (or revalidated in the case of validated systems). This the fewer the vendors you select, the lower the costs.
    • Does the vendor provide validation services?
  • What is the true cost of ownership?
    • Yearly Licensing fees. Is it licensed per module? Is it licensed per module/per seat? Will you end up paying for extra seats for a given module that your organization never uses?
    • Implementation/configuration costs
    • Integration costs
    • Support costs (both internal and external)
    • On-Prem vs Cloud-based Hosting costs. Does the vendor provide a discount for cloud-based hosting?


In addition, to each of the previous options, you may find it necessary to buy multiple solutions, and integrate them together. You may also have internally developed applications that require integration.

  • Do you have experienced programming staff to support this?
  • Do the systems you selected have publicly available APIs (Application Programming Interfaces) that you can write to? (see Frequently Asked Questions for more details).
  • How will this affect our upgrade costs if each integration has to be re-tested whenever the vendor rolls out an upgrade?

Read more of the ELN/LIMS Blog Post Series

Need help getting started with your ELN or LIMS project? Contact us

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Pipeline Stories: A Scientist Walks Into A Bar

Pipeline is Aspen Biosciences premiere application for managing drug discovery projects. It started as a simple dashboard for visualising the drug discovery pipeline, and has grown into what some project scientists characterise as “JIRA for Pharmaceutical Projects”. That growth has been driven largely by conversations with scientists who’ve found themselves in the position of having to manage drug discovery projects and needing a tool that was both lightweight and user-friendly.

In the previous series of blog posts, we talked about Design Thinking and how it can be used to create research-oriented software to support drug discovery. In this series of blog posts, we’ll take a look at some of the stories that scientists shared with us, and show you examples of how we translated conversations into new functionality for Pipeline.

A Scientist Walks Into A Bar

Here in San Diego we are blessed with a number of organisations designed to help the entrepreneurial scientist translate their ideas into businesses. One of these organisations is the San Diego Entrepreneur Exchange (SDEE). Every month they host a Happy Hour meeting at a local microbrewery. It’s a great way to unwind, and network, and for us it’s a great way to meet scientists and listen to their stories.

Photo from the recent Portfolio & Project Manager’s Meetup

At one such gathering a few years ago, I ran into a Director of Discovery Biology at a small drug discovery company (let’s call her Jane — not her real name, gender or title). I introduced myself, and mentioned that I write software for drug discovery and since I’ve always been interested in the process and tools that companies use to select their targets I wanted to learn more about how they selected targets at her company.

Jane’s company, is a small drug discovery company with about 50 scientists on staff that had been in business for over 14 years and had successfully partnered with larger companies to get their drugs to market before finally being acquired. Even after the acquisition though, the company still continue to function as though it were a small biotech. So I was interested to hear how they managed the target selection process in this blended environment.

I began by asking her how the target selection process had changed over the years. “What tools are you using now to manage the drug target selection process?”

“A few years ago we bought a license for a product by a local company. [I’ve omitted the name to protect the innocent]. The product has changed hands over the years and it’s become almost a kitchen sink application.”

“One of the things they tout, is that ‘we do all the homework for you, so you don’t have to. We go to all the conferences. We research all of the targets and the pathways, we curate all of this information for you and save you all that time and money. And for all of that we charge $50,000 a year’.”

“And while I appreciate the amount of work that goes into curating all of that information, it’s a little disingenuous to imply that we can simply delegate that work to them and hope that they’ve done it properly. We still need to research those targets ourselves, we do a deep dive into the target and the indication. We look at disease biology, we look at clinically relevant variants, we look at a half-dozen pathway databases. We look at specialist databases like COSMIC and TCGA (The Cancer Genome Atlas) for specific cancer indications. We look to see what drugs are in development for the target. We do literature searches in PubMed and read lots of articles. We go to conferences, we create internal target profiles, and presentations. But $50K is still pretty steep for something that only one person might use 2-3 times a year, and for work that we’re going to do anyway. $50K would keep us in reagents for a few months. We could buy another microscope — something we’d use every day.”

“So what were you doing before? How were you organising the information,” I asked.

“We used PowerPoint and SharePoint for a while. We’d create a presentation template to help us pull the information together. You still have to go to all of the sites, review the information and curate it. But at least the information was curated in a single consistent format. ”

“What made you switch from SharePoint,” I asked.

“With SharePoint, only one person at a time could work on the target profile. We have a number of people in our group and we needed to divide the work between us. But splitting the work up between the members of the team had its consequences as well. When we were first getting started, we realised that we weren’t doing consistent searches in PubMed. Now we teach target reviewers to do searches consistently. They can still create their own custom searches, but we want to make sure that there’s at least a minimal set of searches being done, and that the search criteria are consistent from project-to-project. ”

“But the real problem with SharePoint was that it didn’t understand biology. We wanted to know the Gene Ontology terms for the target. We want to know about the domains that the target has. We want to know which pathways a target plays a role in. We wanted to be able to look across our portfolio at our projects see if there were similarities between projects that we’d already worked on.”

“And now? With your new application? Do you feel that those issues were addressed” I asked.

“To be honest it feels like we’ve traded one set of problems for another. We see these curated views, that aren’t editable. We can’t emphasize that this subset of the available information is pertinent to our project, and this other set isn’t. We need a better alternative.”

Translating The Conversation Into Code

One of the key requirements that Jane shared with us was the need to provide a single point of entry for a project. There needed to be a way to import target-related data from multiple sources to create a single curated view of the target. To do this, we implemented a search tool that lets the user easily import data from UniProt, PharmGKB, EntrezGene, PubMed, Protein Data Bank, ChEMBL and many other sources with a single query.

Documents and Presentations
In Jane’s company they use Google Docs to collaborate on documents, presentations and spreadsheets. They made the switch to Google Docs after a particularly tense day when a team of researchers were trying to prepare a presentation highlighting results from their latest project. The problem was they were attempting to collaborate on the same presentation by sending copies of it back and forth by email. Versions of the document were getting muddled, slides which had been added, disappeared in the next version, back and forth it went and tensions began to rise.

Cloud-based office applications like Google Docs and Office 365 have become more ubiquitous in pharmaceutical companies over the years but in many cases users aren’t made aware that they can actually simultaneously edit a document. At Aspen, Dimitri and I use this feature to collaborate on proposals and presentations while chatting with colleagues in San Francisco or Boston.

In both Google Docs and Office 365, users store the URL for the document in Pipeline so that they can easily get to the information they need. Document-level security is managed by either Google or Microsoft.

In scenarios where a document is authored by a single user, the document can be uploaded into a private Google Drive that is part of Pipeline’s backend infrastructure. In cases where the customer uses a document management system for sharing, signing and managing document workflows, users can publish the URL for the document in Pipeline along with document metadata such as a title, description and tags used to classify the document.

Pathways, PubMed and More
A significant portion of Jane’s time is spent in portfolio management. In many companies with large drug development organisations, the focus of portfolio management is financial, competitive and logistical. In drug discovery, the focus of portfolio management is primarily scientific and can be boiled down to two questions – what is the role of this target with respect to the indication, and how amenable is it to therapeutic intervention.

To answer these questions requires information from a variety of different sources to be integrated.

  • EntrezGene is an NCBI database of genes and their sequences, sequence annotations and functions.
  • ChEMBL is a database of targets and drugs created by the EMBL. Information from this database tells researchers about the drugs currently available or in development for a given target
  • GeneRIF – these References Into Function provided by NCBI’s EntrezGene database, are a collection of papers that describe the role of a gene with respect to a variety of different indications.
  • UniProt – is a database that contains information about proteins and their functions.
  • OMIM – is the Online Medelian Inheritance In Man database contains information about genes and their roles in various indications.
  • Protein Data Bank (PDB) – is a database of protein structural information that provides researchers with 3D models for drug targets.
  • Gene Ontology information which describes the biological function, molecular function, and cellular localisation of genes and their protein products.
  • PharmGKB is the Pharmacogenomics Knowledge Base which contains information about the target and how existing variations affect the efficacy of known drugs
  • PubMed – is a massive database of millions of academic papers
  • Pathway information from sources like KEGG, Pathway Commons, WikiPathways and the NCI’s Pathway Interaction Database are used to help researchers understand the role of the target with regard to biological networks.

By providing all of this information in a single place that was easily curateable by project scientists, Jane’s team was able to create the kind of collaborative working environment that she had been looking for. And the Pipeline Stats View let her look at projects across her entire portfolio for areas of commonality that they might be able to exploit.


Read more of the Pipeline Stories series.

Need Help Getting Started
To find out more about what Pipeline, and what we can do for your research organisation, contact us.

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Follow The Sun

Every company you work for teaches you lessons. Early on in my career, I worked for a global oil & gas company. Agility isn’t typically a word one normally associates with global companies, but this was different. This was agility on a global scale.

There are often cases where you need to analyze a large amount of data in a short amount of time in order to make a critical business decision. One advantage that global companies have is the ability to create “Follow The Sun” projects that leverage the global nature of companies, and the 24 hours in a day.

A typical project might start in The Hague, and 8 hours later transition to a team in Houston; and 8 hours after that to a team in Kuala Lumpur. In those days, only large international companies had the pipes and data centers needed to support that kind of work. But the advent of cloud computing created a level playing field that now allows any company to work with partners anywhere in the world.

At Aspen Biosciences, we’ve applied the lessons around “Follow The Sun” projects and used them to help deliver projects to customers. By partnering with companies in Nepal and India we’re able to scale up to tackle large, time-sensitive projects.

But we’re not alone in this regard. In the drug discovery industry, startups are able to leverage partners in China and Europe to advance their projects quickly using services like and ScienceExchange to identify the resources they need.

In addition to using the “Follow The Sun” approach, we also cloud-based tools like Pipeline to make it easier for global companies to work with partners regardless of their location. Contact us to learn more.

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Missed Opportunities in Life Science Podcasts

In a couple of recent posts I wrote about the current landscape of life science podcasts, and highlighted some of the consistently highest rated ones, and some of the podcasts that deserve a second look.

One thing has become readily apparent though, is that even with the variety of podcasts currently available, there are a number of “holes” in the marketplace that could be addressed and would stand a good chance of finding an audience.

Opportunity 1 – This Week In Cancer
Vincent Racaniello’s This Week In Microbiology and This Week in Virology are both outstanding podcasts and really highlight the value of bringing recent developments in a field of study to both a professional and a lay audience. These podcasts strike that balance well, and I think there’s a real market for a similar “This Week In Cancer” podcast. Something which highlights discoveries in a wide range of cancers, and draws on the large cancer research and drug discovery communities.

While are some excellent podcasts that focus on cancer, they often focus either on a specific indication (like the Investigating Breast Cancer podcast) or a specific therapeutic classes (like Novel Targets). This may be an indication that cancer is too broad a topic for any one podcast to really do it justice, but having a podcast that draws on experts from the major NCI cancer centers, pharmaceutical companies, and academic research centers would bring a multidisciplinary perspective to cancer.

Funding sources for such a podcast could come from pharmaceutical companies, cancer centers, biotech companies

Opportunity 2 – Focused Nature Podcasts
While I enjoy the weekly Nature Podcast, I find that it broad and unfocused, since it draws on a number of Nature journals and general science news. I would really like to see smaller more tightly focused podcasts from Nature. Imagine a Nature Cancer podcast that draws on materials from Nature Cancer and Nature Cancer Reviews, or a Nature Biotechnology or Nature Drug Discovery podcast. Something that does a deeper dive into these topics than your average general science podcast can do. We have some really great science podcasts like Science Friday, This Week In Science, The Guardian Science Weekly, and BBC Inside Science podcasts so adding another general science podcast doesn’t really make much sense. A podcast which is much more focused on the research that appears in Nature journals would make more sense.

Opportunity 3 – The Business of Life Science
Notwithstanding the rather spotty publishing history of the FierceBiotech podcast, we need a podcast that covers the business of life science and publishes on a regular basis. News about the players both big and small in the pharmaceutical and biotech industries. News about the deals, the discoveries, and the personalities. There’s plenty to discuss, and plenty of print resources to draw on including Xconomy, FierceBiotech, FiercePharma, PharmaTimes, and Forbes just to name a few.

Opportunity 4 – Community Driven Podcasting
In the US, there are 3 major biotech centers: Boston, San Francisco, and San Diego. Having a podcast that focuses on each center with news and interviews with representatives from companies in those areas would make it easier for people to keep up with the latest news on local companies, and identify potential partners.

Posted in Cancer Research, Drug Development, Drug Discovery, Informatics, Social Media | Tagged | Leave a comment

Mistakes Life Science Podcasters Make

In a previous blog post, I surveyed a wide variety of industry podcasts to give you an idea of the breadth of podcasts available to address the needs of the life science community. We have everything from general science podcasts to journal podcasts. These podcasts can turn your daily commute from a time suck into a valuable learning experience.

During the course of evaluating the podcasts, I came across a number of issues that podcasters were running into. Issues that can make the difference between attracting the right target audience, or driving them away:

  • Be engaging — It’s a mistake to simply read off the abstract of a journal article, including all of the stats in the article, and expect the audience to be engaged (OncoTarget).
  • Learn the vocabulary — Drug discovery can be a challenging area to discuss on a podcast. The terminology is often very specific to the industry, therapeutic area, or indication and is rapidly changing with the pace of discovery. The audience has only your voice to go by, so when you fumble the name of a drug, or a disease process (and do it consistently through the entire podcast) it becomes the thing your audience focuses on, rather than the information that you’re trying to communicate.
  • Use conversations — Podcasts are ideal vehicles for conversations. The journal podcasts that do best, consist of conversations with scientists whose papers were recently accepted for publication. The lead author is uniquely positioned to talk about their research, and the best podcasts use conversations to help communicate the value of the research and to tell an engaging story.
  • No eating during recording — In one particularly bad episode of OncoTarget, I listened to one scientist unwrap and eat his lunch, while his partner continued to engage with the interviewer. The other scientist forgot to turn off notifications on his computer, so that every e-mail or IM he got resulted in a ding, and at some point during the conversation, they started to experience bandwidth problems so the remote interview got a bit garbled. Don’t attempt to record in a cafeteria between sessions at a conference, the results won’t be worth listening to. Pretend you’re the BBC and be professional about your product.
  • Be consistent — A podcast is not something that you do for a couple of months, and then abandon, and/or resume a couple of years later (I’m talking about you FierceBiotech). The life sciences industry covers a wide variety of sins, and there is a constant stream of new discoveries that need to be discussed. While this may point to an initial difficulty in finding an audience, consistency of publication is essential to finding that audience.
  • Be like the Pope Pope Francis famously said that he had to be where his parishioners were in their faith journey in order to engage with them. For podcasters it’s the same thing. It doesn’t do you any good to publish only on SoundCloud, if your listeners are on iTunes and Stitcher. In fact, neglecting one of these platforms can cost you audience reach, and advertising revenue.

Who’s Doing It Right

So, who’s doing it right? Here are a few podcasts that are consistently ranked high in the ratings, and produce quality podcasts:

Hidden Gems

Who’s doing it right but still hasn’t found their audience yet?

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Tinkering with the Latest Cytoscape Release

In previous posts[1,2] I’ve described some of my experiences with Cytoscape including a short wishlist of features.  In this latest release I was pleased to discover that a number of those issues have been addressed.


Exporting Networks As JSON
One of the first things on my wishlist was a simple way to export a Cytoscape network as JSON.  This was driven in large part by some experimentation with the Cytoscape.js javascript library. I wanted to quickly assess the capabilities of the Cytoscape.js library without spending a lot of time manually building a network in JSON.

With the new functionality, you can now export your network as JSON, and then import it into your web page.  This is a nice way to make your network viewable by colleagues and potential collaborators without forcing them to download and install the desktop version of Cytoscape.

To export the network, simply select File/Export/Network… from the menu.  The Export Network dialog will then appear. Select the Cytoscape.js export format and enter the name of an output file.

You can also export the styles that you used in the desktop version of Cytoscape, by selecting File/Export/Style… When the Export Style dialog appears, select the Style for cytoscape.js export format and enter the name of the output file.

Exporting the network as HTML
The second thing I asked for was a way to further simplify this process by allowing the user to export the network using a simple HTML template.  Rather than making the user create their own HTML page to display the data, you simply export the results as HTML and include the JSON in the content of the web page.  This makes it easy for people with limited HTML skills to produce something that can be easily viewed in a browser.  If you’re a wiz at HTML and templating, you can modify the template to produce fancier output.

Visualising JSON
Cytoscape supports 2 JSON formats — CytoscapeJS JSON, and CX. These formats bring with them the possibility that developers could use a text mining library to identify protein-protein interactions from literature, and write the results out as JSON so that they can be easily visualised in both the desktop and web versions of Cytoscape.



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Red Flags in Drug Discovery

A few years ago, Luke Timmerman of Xconomy wrote about the 21 Red Flags in biotech investing and Sally Church of the Pharmastrategy Blog wrote a related post on Red Flags in clinical trials and cancer research.  Here are a few additions of my own that I’d like to add to those lists.

Context is Everything
Target identification itself is something of a black art, because in many cases you have a really incomplete picture of the target space for a particular disease.  The literature may only tell half the story.  Most of the papers I’ve been reading lately identify one or two novel genes or pathways and associate that gene or pathway with pancreatic cancer.  When I read the Methods section, the authors have a tendency to natter on about standard protocols they followed, and neglect to tell us anything about the patients profiled in the paper. This leaves me with some nagging questions:

  • What stage was patient in when the sample was taken?  What I really want to know is can a particular result (a mutation or a differentially expressed gene) be tied to a specific process known to be in play at a given time in the progression of the disease.
  • Was the patient from a family that had a history of one of the 5-6 known syndromes for pancreatic cancer? Do the results reflect one of those syndromes? [PMID: 23187834]
  • What parts of the tumor were sampled? Tumors are rarely if ever homogeneous in nature.  Colonies of cells continue to accumulate mutations as they attempt to gain the functions they need to invade local tissue and to metastasize.  This means that if you take multiple samples from a tumor you are likely to get different answers, and those variations will give you a clearer picture of the tumor biology and progression.  The more complete the picture, the greater your chances of success in clinical trials.
  • What was the state of the primary tumor area?  Do we see signs of local invasion?  If so, in what tissues, and how does that correlate to the genotyping or gene expression data we’re seeing?  Does a piece of tumor located near the liver show signs that the tumor is preparing to invade the liver? Does the primary tumor show signs of invading the celiac nerve plexus?  Do we see a corresponding signature for perineural invasion?
  • Do we have distal metastases?  If so, where?  Were samples taken from the metastases and compared with primary samples? [PMID: 20981101]
  • Was the patient a smoker?  If so, how much? Do the results show any connection to known smoking-related mutational signatures?[PMID: 19351817]
  • Were the samples taken prior to treatment or after treatment, or both?  If both, what was the effect of the treatment both at a phenotypic level, and at a genetic level?
  • Were any circulating tumor cells also sampled?  How does this compare with the primary tumor?  How do those samples compare with one another? How do they compare with mets?  Do certain CTCs genetically resemble site-specific mets?  Is this CTC destined for a brain metastasis or a met in the omentum?

In general, I’d like to see more papers attempt to connect the dots not only between genes and pathways, but to specific processes in cancer. That connection to a disease process discloses the real value behind the research.  Without it, it’s like reading a murder mystery and realizing that someone ripped out the last chapter. You feel cheated.

Lack of Reproducibility
Over the past few years pharmas have begun to depend on a greater extent on the research of external collaborators in academia and startup companies.  In the case of the former, it’s been a real challenge to reproduce some of the results that pharmas are hoping to place a bet on.  In academia, the emphasis is on publishing — and successful results get published, experimental failures don’t.  This means that you often see results where the experiment failed 5 times, but succeeded on the 6th; and it was the 6th that was included in the paper.  In industry, an experiment has to work 10 times out of 10 in order for someone to bet the “pharm” on it.

Getting The Right Advice
When selecting a target (and an indication for that target) it’s important that you get good advice from people who work in that discipline.  Stephen Covey, the late author of the book, “The Seven Habits of Highly Effective People”, used to say, “start with the end in mind”.  And in this case, that means talking with clinicians, and letting the disease guide the discovery.

From the clinicians you want to know what constitutes an underserved area.  For example, your initial inclination might be to attempt to tackle metastatic disease in pancreatic cancer. However, a recent study showed that it was actually the degree of local invasion that was a greater predictor of mortality in patients.  And this makes sense if you think about it.  If the tumor is invading parts of the digestive tract, and into the sympathetic nervous system, the quality of life of the patient is rapidly diminished and the amount of pain they experience is increased.  Since perineural invasion is a common event in pancreatic cancer patients, and most patients spend the last few weeks on large amounts of pain killers, it might be a better short-term strategy to interfere with perineural invasion, and have a longer-term research program focused on a cytotoxic therapy.

Ultimately, you want to end up with something that clinicians want to prescribe to their patients.  And the more you know about the problems they’re dealing with, the more likely you are to have a winning product.

Posted in Cancer Research, Drug Discovery, genomics, pancreatic cancer | Tagged | Leave a comment

DB Cooper Stories in Cancer


D.B. Cooper

Last year the news was all abuzz with new evidence that was uncovered by amateur investigators looking into the most infamous hijacker in aviation history, a man known only as DB Cooper. The investigators found traces of material on his tie that was connected to Boeing’s SST development. But the story leaves more unanswered questions than explanations. What parts of the SST did the flecks come from? Engine, fuselage, avionics? Did the flecks come from parts that were manufactured by Boeing or by one of its subcontractors on the project? Did they look at the employee records of Boeing during that time period to see if anyone matching DB Cooper’s description worked for Boeing?

It started me thinking about a number of the stories in cancer research that were equally frustrating, in that the authors failed to tell, what radio personality Paul Harvey liked to refer to as, “The Rest of the Story”.

The story that came readily to mind was a series of articles which identified several species of bacteria which were over-represented in the oral microbiomes of pancreatic cancer patients[1-7] and another study looked at the gut microbiomes of pancreatic cancer patients[5].

Two different sets of studies were performed by different organisations to identify species of oral microbes associated with pancreatic cancer. In one study, the authors found that 2 species of bacteria (Neisseria elongata and Streptococcus mitis) were over-represented in the oral microbiome of pancreatic cancer patients. And the author speculated that the bacteria likely did not play a causative role in the etiology of the disease.

Two studies with different conclusions, and different bacterial species. Which opens the door for a third, as yet unwritten study, to analyze both results and either confirm or fail to confirm one of the previous studies.

The unanswered questions in these studies are:

  • How does pancreatic subtyping affect the results seen in these studies? Could both studies be right, and one set of bacteria is more prevalent in one subtype of pancreatic cancer? Is there a link between the immunogenic subtype of pancreatic cancer and the presence of these species?
  • Do these populations change throughout the progression of the disease? Do we see a gradual increase in the population as the disease progresses? How does treatment affect the bacterial populations? Are there certain treatments that cause different species to predominate?
  • And perhaps the biggest unanswered question is why is this happening? What role do these bacterial species play with regard to pancreatic cancer? 

One tantalising idea that arose from this research is that one day your dentist’s oral cancer screening could include a simple test to detect pancreatic cancer at an early stage.



  1. Fan X, Alekseyenko AV, Wu J, Peters BA, Jacobs EJ, Gapstur SM, et al. Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study. Gut. 2018;67: 120–127.
  2. Michaud DS, Izard J. Microbiota, oral microbiome, and pancreatic cancer. Cancer J. 2014;20: 203–206.
  3. Bracci PM. Oral Health and the Oral Microbiome in Pancreatic Cancer. Cancer J Sci Am. 2017;23: 310–314.
  4. Ertz-Archambault N, Keim P, Von Hoff D. Microbiome and pancreatic cancer: A comprehensive topic review of literature. World J Gastroenterol. 2017;23: 1899–1908.
  5. Wang C, Li J. Pathogenic Microorganisms and Pancreatic Cancer. Gastrointest Tumors. 2015;2: 41–47.
  6. Meurman JH. Oral microbiota and cancer. J Oral Microbiol. 2010;2. doi:10.3402/jom.v2i0.5195
  7. Olsen I. Oral microbial dysbiosis precedes development of pancreatic cancer. J Oral Microbiol. 2017;9: 1374148.
Posted in Cancer Research, microbiome, pancreatic cancer | Tagged , | Leave a comment