gtaylor's blog

10 Mar

TSL Status March 14, 2006

Published by gtaylor


general open research

Presentation given at Stanford

Marc A. Marti Renom is by far our biggest evangelist and his efforts are making a big impact. He recently gave a presentation at Stanford talking about the goals and objectives of The Synaptic Leap and Tropical Disease Initiative. Marc posted a brief description as well as the presentation he gave this tsl post. The great news is that people at Stanford are emailing other people participating on The Synaptic Leap and they looking to find the appropriate way to get involved. Mat posted a bit of that exchange here: Ways to get involved and the Stanford connection.

Marketing observation and future objective

An interesting observation from this is that shortly after Marc gave the presentation, I noticed a spike in user activity - both more people browsing as well as a few new registered users from Stanford as well as people from Germany and Italy. We saw a similar spike in activity after Marc spoke at a QB3 Neglected Diseases symposium. In fact it was after the symposium that we were blogged about on World Changing. That in turn led to a spike in user activity.

23 Feb

New Feature for Resources Needed

Published by gtaylor


general open research

About two weeks ago Marc and I were about how we needed to make the site more actionable to get people knowing what they can do to help. I therefore have added a new menu item on the left called resources needed. When you go to that page, you will see a list of postings for resources. At the top of the page is a "sticky" page that describes for readers what they are seeing, how they can volunteer and how they can ask for help on their project. Think of this as the classified for open source biomedical research.

10 Feb

TSL Status February 10, 2006

Published by gtaylor


general open research

It’s been too long since my last status update. A lot has been accomplished.  


We Added the Schisto Community to our Pilot Site

Going from one research community to two research communities took quite a bit of redesigning. Since our goal is to ultimately be able to support any disease-focused open research, this was a very important step.  We iteratively worked in our development environment, prioritized changes and evolved to what we have now on our pilot site. Our current organizational approach will allow us to scale up to another 20 or so research communities without requiring additional enhancements and site redesign. Let’s hope we can be so fortunate within the next year and that we use this time to gain more insights into the unique needs of open scientific collaboration.

I’d like to take this opportunity to give special thanks to Steve Maurer and Mat Todd for driving the new pilot site content and look and feel.  They wrote copy, and gave me feedback nearly every day for about a month.  David Sayed also made significant contributions, writing copy and correcting my grammatical errors.  These contributions made a big difference and I believe the pilot site is far better thanks to these people. 

  • More information on schistosomiasis
  • More information on the changes that took place as well as those still on the list is logged in this blog entry.

We Have More Industry Domain Advisors

My background is software and business.  Therefore naturally, my initial advisors have been heavily weighted with software and business people – it’s who I know.  Fortunately, as we gain momentum, the pendulum is shifting.  I am now getting lots of input and advice from biomedical experts.  This is critical.  The following people are experts in the biomedical field, believe in our mission, and have agreed to continue to guide us in the right direction:

10 Feb

Archived Status Notes for 2005

Published by gtaylor


general open research

You may read the comments for this post to see the TSL community status notes for 2005.

08 Feb

Writing for the web

Published by gtaylor


general open research

When writing our project descriptions and other posts to the site, we all need to keep in mind that we're communicating over the web.  This isn't the same as writing a paper for publication. 

Jakob Nielson, usability gu-ru, has written a piece on this and it's posted to Sun's web site.  I thought I'd share: Writing for the Web.  Some of it doesn't really apply to what we're doing but some does.  The points I think that are pertinent:

  • 79% of users scan while reading on the web only 16% read word-for-word (so what happened to the other 5?)
  • write for scanability - this means conclusions first, topics separated by headings, important things should be in lists
  • use simple sentence structures.  People are impatient when reading online and don't want to wade through long sentences

Sample Headings for a collaborative project:

  • Overview of the project 1-2 paragraphs
  • Who's Involved, gotta give credit where credit is due
  • Describe how others can get involved - make it actionable
  • More project details perhaps on the page or perhaps attached as ppts/word docs/ excel spreadsheet for issues and to-do tracking...
30 Jan

Story Behind the Name

Published by gtaylor

The information superhighway of the human body involves communication of neurons between cells across a synaptic cleft. Neurons are composed of dendrites and axons. The dendrites receive incoming messages so that the cell may absorb the information. This information may then be passed on, traveling down the axon and then sent on to the next cell. Some refer to this as the synaptic leap.

image of synaptic cleft 

Neuroscience teaches us that we are born with most of the brain cells and neurons that we need. Yet, when we are first born we don’t even know how to focus our vision. It is believed that our synapses fire a bit randomly at first. With experience and repeated connections, new dendrites form and the synaptic leap becomes more efficient. Based on our genetic make up as well as the stimulus around us our brain makes connections and we learn.

This is exactly what is happening on the Internet today. It is slowly evolving from a random soup of people and ideas. New collaborative pathways are being forged and connections are being made. The human race is on the verge of doing some very big things.

The Synaptic Leap is all about enabling new collaborative pathways for biomedical researchers. The research talents brought to bear on medical issues should no longer be constrained by geographical boundaries. The sum of the connected whole will be much greater than the sum of the disconnected parts. It is our duty to mankind to provide the collaborative infrastructure that connects scientists willing to make the leap to accelerate the research process.

13 Jan

News sources for TSL

Published by gtaylor


general open research

One of the services The Synaptic Leap provides for its users is the aggregation of news that is relevant to our research communities, e.g. malaria and schistosomiasis.  You can see this under the News Feeds link in the navigation block. 

I'm not a scientist, just a computer geek.  Therefore I could use your help in making sure we are getting content from the best sources for you.


  • It must produce an RSS/XML feed.
  • It must either be a source focused on the research topic e.g. Malaria Journal, or must support an RSS feed for a specific tag or search key word. I don't want to boil the ocean and bring in all recent science news from journals.  That would cause our site to lose focus and purpose. But I will gladly bring in content from a specific journal if it will support search/tag specific RSS feeds.

By meeting this criteria, it allows me to create research specific aggregated news feeds for the community. 

Sources for News Feeds I've Found Meeting Our Criteria (in alphabetical order)

Good Sources For Content but I Can't Find Topic Specific Feeds

  • Cell - Offers RSS feeds for latest articles by journal but I can't get tag/search specific feed for malaria, schisto...
  • Google Scholar - great search engine but I don't see how to get an RSS feed from search results.  But given the power of Google Scholar, I've decided to add a block for it in the upper right.  If you register, you may choose to remove the block by configuring your personal profile.
  • Nature - Offers RSS feeds for latest articles by journal but I can't get tag/search specific feed for malaria, schisto...
  • Science - I can't even find their RSS feeds, surely I'm missing something...
  • PLoS - Offers RSS feeds for latest articles by journal but I can't get tag/search specific feed for malaria, schisto...

What We Need From You 

This is your community; participate to make it better.   

08 Jan

Changes to Support Multiple Research Communities

Published by gtaylor


general open research

Great news!  The Synaptic Leap will roll out a new research community for schistosomiasis very soon.  This will require evolving our pilot site from a single research community to a site that supports multiple research communities.  We will also create a TSL non-research oriented community for general open-source biomedical research discussion and tools and we will evolve this to become our only site to communicate with you. 

We have a prototype of this new infrastructure on our development site. We are getting feedback from our advisors and research community leaders and are improving the general site usability too.  As change ideas and content firms up, we will slowly roll out the changes. 

I will do my best to keep you informed on these upcoming changes by evolving the information on this page. This list will evolve in terms of what's to be done as well as what is already done.  Check back periodically to see where we are in the process.  Oh yes, and feel free to login and add comments to give us feedback on these changes.

Thanks in advance for your patience and your input.

Primary Project Participants 

  • Ginger Taylor
  • Mat Todd
  • Steve Maurer

Upcoming Enhancements and Changes

  • Add email subscriptions - not everybody uses XML/RSS feeds to stay informed; email is still the primary tool for lots of users
  • Get the images module working and file type support for ChemDraw.  This will be especially important for the organic chemists who are to start working on the schisto projects. 
07 Dec

Current Pilot Projects - Malaria Community and Individual Based

Published by gtaylor

My current vision is that The Synaptic Leap will evolve to allow any community to be opened for any given disease.  And once opened a community moderator would be responsible for configuring some basic community resources:

  • the resource page - linking users to other research tools on the net
  • the RSS sources for researching that disease - e.g. Connotea, Technorati, CiteULike...
  • at least one discussion forum to debate topics and projects for the disease - the community moderator can decide if more are needed.
  • a projects page to link  users to ongoing as well as completed projects regarding the community disease

Individual users could participate in more than one research community.  Blog pages would belong to the individual, but could also be tagged to be published within a given research community.

18 Nov

Embrace the chaos!

Published by gtaylor

A Greek friend of mine once told me he didn’t believe in voting. He said that the Greeks invented democracy but had evolved past it to chaos. At the time, I thought he was just being eccentric and didn’t push him on the subject. However the statement was odd enough to stick in my brain. After all, Petros doesn’t say things just to hear himself talk; he’s usually thought long and hard about such things before saying them. As I’ve been contemplating how to find cures to diseases more quikly, I’ve decided that chaos is the next evolved state of scientific and medical research and is what we should help unleash to both find cures more quickly as well as lower the cost of discovery.