Open Notebook Science

Sunday
Thinking about our recent posting  regarding project and document management, along with a number of postings on open source data, people might be interested in learning more about a movement that takes open source to a basic level.  As described in Wikipedia:

Open Notebook Science is the practice of making the entire primary record of a research project publicly available online as it is recorded. This involves placing the personal, or laboratory, notebook of the researcher online along with all raw and processed data, and any associated material, as this material is generated. The approach may be summed up by the slogan ‘no insider information’.

While not everyone thinks this is a great idea, a number of labs in a variety of disciplines have begun to embrace the concept.  Similar to the Creative Commons movement, there are a number of ways to implement open science in your lab (with associated logos, of course!).

So, does open notebook science have a place in biomedical research, and does it have a role in translational science?

Further reading:

Pharma and Social Media

Pharmaceutical companies continue to struggle with patient interactions in today’s social media environment.  While a number of pharma and biotech firms have a presence on social platforms, the conversation has traditionally been one-sided.  The companies speak, and the consumer can only listen.  However, that’s now starting to shift.

Pharma brand marketers that disable comments on their Facebook pages are in for a change. As predicted, Facebook will no longer allow pharma brands – which are typically highly risk averse when it comes to discussions about their drugs and products in social media environments – to turn off commenting on their pages.[via]

Part of the challenge is a regulatory one.  Industry continues to wait for guidance from the FDA on how social media should and should not be used.  Although the FDA held a hearing on this topic back in 2009, they continue to delay issuing any guidance (which was most recently supposed to be available in Q1 2011, but that didn’t happen).

For now, it seems that pharma and the social media providers must continue to work this out themselves.

Scientists, Social Media, and Web 2.0

Here are two interesting postings regarding science and the “new web”.

First, how do most labs view the use of social media?  Not very highly, if you believe the results from a recent survey by Lab Manager Magazine:

Laboratories are at the forefront of research and analysis. But when it comes to communication, they are followers rather than leaders and can be very slow to adopt innovations. The use of social media is a case in point, as a recent survey of nearly 200 lab managers revealed. There are six good reasons for labs to explore the opportunities offered by the social media…

This could also be part of a bigger event, which some say is the demise (or maybe transition) of science 2.0.  As David Crotty argues in “Not with a Bang: The First Wave of Science 2.0 Slowly Whimpers to an End“:

The Nature Network launched in 2006, organized around researchers in Boston, then went global in 2007, five years ago. It perhaps offered the high-water mark in terms of the irrational exuberance by publishers and other companies in building big Web 2.0 tools for scientists. For a time, the widespread adoption of these tools seemed inevitable, and business models were an afterthought when investing in revolutionary new technologies.

Five years on, reality has reared its ugly head, and, as is often repeated here at the Scholarly Kitchen, culture has trumped technology. It turns out that what works well for some cultures does not immediately translate into success in others. Rather than focusing on the needs of the research community, much of what passed for Science 2.0 was an attempt to force science to change — to make the culture adapt to the tools rather than the other way around.

Do we see either of these phenomena in our day-to-day interactions?

World’s first crowdsourced clinical trial?

PatientsLikeMe, an online community where individuals can track their conditions and compare symptoms with algorithmically-similar patients, just published in Nature Biotechnology what it calls  “a patient-initiated observational study refuting a 2008 published study that claimed lithium carbonate could slow the progression of the neurodegenerative disease, amyotrophic lateral sclerosis (ALS).”

The story in the Wall Street Journal adds:

“A new clinical trial found that lithium didn’t slow the progression of Lou Gehrig’s disease, but the findings released Sunday also showed that the use of a social network to enroll patients and report and collect data may deliver dividends for future studies. The study was based on data contributed by 596 patients with the disease, formally called amyotrophic lateral sclerosis or ALS. By showing that the drug didn’t have any effect on progression of the condition, it contradicted a small study three years ago that suggested such a benefit was possible. The new study, published online in the journal Nature Biotechnology, represents an early example of how social networking could play a role in clinical trials, an area of medical science with strict procedures that many would consider especially difficult to apply in the online world.” [via]

Read more:

Turning Science Communication into a Dialogue

The Stanford School of Medicine managed to promote science stories broadly without issuing any press releases. At the national CTSA Communications Meeting, John Stafford, New Media Strategist at Stanford, shared some insights how this worked.

Depending on the science story, they posted what’s newsworthy on their blog Scope , Twitter, Facebook, Flickr, and – very important – they successfully leveraged the informal relationships with their “blogger friends”. As a result, some of their stories made it into leading science magazines and newspapers.

But the story doesn’t end here: John also demoed a few online monitoring tools to measure media reach and brand leadership. These tools provide dashboards for monitoring how many and what types of media outlets pick up science stories, and even what attitudes readers have towards those stories. Here is a list of tools that might become useful to some of our organizational initiatives:

  • Radian6: Provides a platform to listen, measure and engage with customers across the entire social web.
  • ScoutLabs: A self-serve, web-based tool that includes natural language processing techniques for sentiment and tone scoring. Read article
  • Sysomos Heartbeat: Provides constantly updated snapshots of online conversations.
  • General Sentiment: Media Measurement Dashboard, Reporting Service, and Data API.
  • Jive: Social media monitoring, engagement, and measurement.
  • Klout: Helps you identify people you might want to start a conversation with.
  • Cotweet
  • Tweetreach

For those who still seek more, Stanford will be hosting a social media conference “Medicine 2.0” in September this year.

Salesforce announces Chatter, social network for the enterprise

As Virtual Home prepares ShareCenter pilots, the enterprise collaboration software space continues to expand. Salesforce recently announced the availability of Chatter, an enterprise social networking application that it has been testing with select customers. Features include user profiles, groups, secure document sharing, status updates, news feeds, and email alerts. Additionally, it allows for building custom Chatter apps, as well as embedding Chatter features into other tools.

Other recently announced offerings in the enterprise collaboration space include Acquia’s Drupal Commons and Cisco’s QUAD which join the mix with established offerings from Socialtext, Jive, IBM, and a sizable list of other players.

Read more about Salesforce Chatter in VentureBeat:

Salesforce says social network Chatter is ready to talk | VentureBeat.

Twitter, revisited….would we or should we use it? Here are 11 Commandments to ponder.

I read a short article this morning about the fact that the Department of Defense issued its social-media policy, and essentiall gave it the thumbs up.   The article goes on to discuss rules of engagement for employees’ use of social media, or lack thereof.  The author puts forth The 11 Commandments of Corporate Tweeting and while these are focused on the use of Twitter in corporate America, I think the 11 are straightforward and rational, and would apply to our setting as well.  A few of them are listed below.

– We can articulate the company vision in 140 characters or less, minus PR puffery and cliché.

– We are willing to give credit to cool, innovative, or thought-provoking ideas, even if coined by someone else.

– We are willing to challenge a potentially destructive position even if our position generates criticism.

Let’s play: An Expertise-Tagging Game

Researcher Jun Zhang and colleagues designed a social game to engage people in contributing to expertise profiling for themselves and their colleagues. In „Expertise­Tagging Game: Identifying Expertise Networks in organizations“ (2007) they describe how it works and a pilot study. Playing the game a user gets certain points when his or her input matches with other users’ input.

Thinking about our newly launched expertise finder system UCSF Profiles, a ‘game’ approach might be an interesting idea to explore. UCSF Profiles builds on a good set of data retrieved from Pubmed and already allows passive networks based on that information. However, active networking mechanisms will be helpful to retrieve ‘local knowledge’ that goes beyond scientific publications.

Here is how the game works: “A person’s expertise tags are presented in a masked tag cloud when the game starts. A user starts playing this game by typing a keyword in the text field following ‘John is a good person to talk to about (X) ‘ once a time. If a tag he sent matches a tag input by that individual or by other users who have played the game, the matched tag is revealed and the user earns some points based on how many other people have also tagged the same keyword.  The goal is to reveal all the masked words in the tag cloud. Top players are named as ‘top connectors’ in the landing page of the game site. Top players for a specific game are also listed in that game’s page as ‘who knows person (X) best’. A network visual-exploration interface  helps people discover the expertise networks around them.” The pilot study showed “that a lot of users were motivated by different fun factors, such as enjoyment of problem solving (revealing the tag cloud) and competition (being a top connector).”

By the way, some senior users expressed concerns of deploying a game into a corporate environment, so the authors  repositioned the ‘game’ as a “system for people to recognize their colleagues by recommending their expertise using tagging as well a means of self-expression by self-tagging and approving peers’ tags”.

And while we are at it, here is a second one: “The Dogear Game” (2007).  Individual players receive entertainment and learn about their colleagues’ bookmarks. The player’s colleagues, on the other hand, receive recommendations of websites and documents of potential interest to them. The numbers are impressive: The game was implemented as a plug-in to a corporate instant messaging client used by over 100,000 employees. Read on.

Enterprise OpenSocial

Heartened to hear that this years Enterprise 2.0 conference in San Francisco features a session on ‘OpenSocial in the Enterprise’.  Mike Gotta, an analyst from the Burton Group, describes some of the issues that OpenSocial needs to resolve to become truly applicable at the Enterprise level – these include the definition of ‘friend’ and single-signon and other authentication issues. 

But his description of the general environment that enterprise developers find themselves in is pertinent to our enterprise – the academic biomedical research institution – and his approach mirrors our thinking.  The question is, how do we tie our (academic/biomedical research-focused) development of research networking products to the trends outside of us?

We need to start designing and implementing social networking platforms that have capabilities to span internal and external audiences. While initiatives that started off in the consumer market may not have the necessary identity, security, and other necessary services – alternatives within the enterprise are often not viable for consumer environments – so we are left somewhere in the middle – with no one particularly happy. Given overall consumerization of IT trends, it seems to me at least, that it’s more viable (in the social computing realm) to start with efforts like OpenSocial and ActivityStrea.ms and evolve them for the enterprise than the other way around.