Archived Status Notes for 2005

10 Feb
Published by gtaylor


general open research

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


I need to migrate the content from our simple blog information site to our more collaborative site and effectively consolidate TSL content onto one site.  Although I don't want to lose my historical status notes, I also don't want to water down the site with a ton of old status notes.  Therefore, I created a comment on this single post for each 2005 status note entry for The Synaptic Leap. 


gtaylor's picture

This is my first entry in the Captain's Log. My goal is to report honest progress, objectives, and issues in a Captain Kirk type style. I hope you find it useful. If you find the name "Captain's Log" too corny, not professional enough, let me know. If you like it, let me know that too. You can register on this site and post comments directly. The Synaptic Leap has done a lot and at the same time, has so much more to do.


  • We have registered our domain name and we're using modhost to host our initial web site as well as some prototypes. And believe it or not, if you give Google our full name, we come up as second on the list. Check it out. Thanks Ken for getting us hosted.
  • We have decided to leverage WordPress as our initial software to construct and maintain our web site as we settle on our community software. We like this because it's easy to extend the content, people will be able to subscribe to our updates via RSS and it's very easy to customize the look and feel (that part not done yet). Rich uses WordPress for his personal site and is the one who has recommended it.
  • We have installed a vanilla copy of Civic Space on our server and we're playing with it a little. It looks to be a pretty solid open-source collaborative community software solution and is a derivative of Drupal with over 300 known implementations. We are by no means set on this solution yet. However, it is one of several we plan to explore to create a fabulous community for The Synaptic Leap. Thanks Rich for installing this for us.
  • We have installed a wiki and source code versioning system at We're using Trac for Wiki, issue log and project management and Subversion for source code control. These applications are favorites of other open-source project efforts. Thus far, I'm quite positive. Thanks Chris for donating the server and your time to administer this site.
  • I've written several web pages as you can see from our "preview site". I've also come up with a wire diagram and basic information architecture for the site. These are not implemented yet and thus we're still in preview mode.
  • Paul and Randy worked together to come up with a first stab of our logo and I think it's a fine first stab. We're going to finalize the design with another graphic artist. Thanks Paul and Randy.
  • Cindy, Lydia, Paul and Sid provided input on our mission as well as general positioning. This positioning is beginning to be reflected in our About page as well as the current draft of a Welcome/Home page. Thanks.
  • Sid has donated the funds and pointed us to a trusted graphic artist that he uses. We plan to use her work to help shape our artistic appeal of the site. Thanks Sid.
  • Sid has also referred us to an accountant who has experience with non-profit organizations. He has agreed to fund a generous amount of their time to help keep our books. At this point they are not under contract. However, they did help give me a few numbers to come up with a projected budget. Thanks again Sid.
  • I recently recruited an Intellectual Property law expert to our cause. Dr. Elizabeth Chadwick teaches IP law courses at Nottingham University and has been added to our About page.

Big Objectives Still In Front of Us and Where We are With Them

  • First and foremost, we need our first customer and we need domain experts on board. I got pounded on this subject by Scott Merkle and Dave Petroni (not an official advisor, but somebody I have a lot of respect for and hope to continue to get input from). These guys are right and I know it. At this juncture I'm trying to build out enough organizational credibility (web site, good advisor list...) to be able to approach somebody. My target customers are:

    I hope to make contact with one or more of these organizations within the next month.

  • We hope to get an official board member from one of those organizations. We also need domain specific input on the type of collaborative processes needed so that we can build our use-case scenarios for creating the collaborative community. This is huge.
  • I'm holding off incorporation until I know more about where I think we can get our funding. It is possible that a serious contributor may want us to NOT go the not-for-profit route. If that's the case, I'm open to forming this organization in whatever manner will get us funded. And, of course, I'm holding off on asking for funding until I have a domain expert/customer on board. We'll get there. In the mean time, I have drafted our Articles of Incorporation and our Bylaws.>

General Comments and Feelings

The development of our web site and the prototypes are going slower than I'd hope. We're all volunteers and doing this on the side. And to be honest, I'm the bottleneck right now. The developers have requested some use-case scenarios for the prototypes to ensure that they're appropriately shaking out our possible open-source solutions. They're right; it's needed and it's up to me to do it. I just haven't had time to do that yet. Reality is setting in for me on how shoestring open-source projects must inch along - especially in the early phases. I hope to get 2-3 of us hired full-time so that we can run full speed and then provide better leverage for our other volunteers. To summarize my upcoming focus: - Get a customer / domain expert to believe we're up to the challenge. This includes getting our web site looking good and getting some prototypes sufficiently ready for discussions with them. - Find out if we can get a big donation from a couple of sources and see how they want to fund it. - From there incorporate. This is Ginger, signing off the Captain's Log.

gtaylor's picture

I was in California for about a week and half and have been busy catching up. The great news is that a lot has been accomplished.


We have our first partner / beta customer. The Tropical Disease Initiative (TDI) is an organization formed with the objective of conducting research via an open source style collaboration to further discovery phase research for developing world country diseases such as Malaria. They have medical researchers, economists and intellectual property experts on board, but were missing collaborative community software expertise. The Synaptic Leap had the opposite problem. We are combining our strengths. The Synaptic Leap will build a beta project room for TDI. We have our first biological expert and research advisor. Dr. Marc Marti-Renom has agreed to be biological expert and research advisor for us. He and I have already met for over six hours as he has schooled me about the typical processes, personalities and concerns of those participating in medical research. We have also discussed the general features and functions of the first TDI project room within The Synaptic Leap as well as ideas for future versions. We will be iterating on these ideas over the next few weeks. We have our first board member. Kara Jurist has a public accounting background with the Accounting and Auditing groups of Deloitte & Touche and KPMG. She has strong process and accounting skills and a passion for advancing medical research. She's already asked to review our budget and I'm quite certain that Kara will keep me on my toes. We have more references and general support. Also while in California, I met with several senior X-PeopleSoft executives who I have worked with in the past. I pitched The Synaptic Leap to them. In doing so, I got experience telling the vision; I refined my message and got some great advice. All were positive to the idea and some downright enthusiastic. A few of these people have also agreed to make introductions and serve as references as we go to apply for grants and funding. This is huge. We have recruited other volunteers. Lynn Cook used to be a photojournalist and still makes money on the side with his digital photography. He has volunteered to take pictures for us for marketing material as well as for web based content and stories. Glenn Mar is a good friend of mine who has quite a knack for inspirational writing. He's agreed to contribute a few articles to The Synaptic Leap - perhaps reviewing and commenting on common news articles surrounding the medical research industry. Glenn is also a semi-professional photographer and may fill in when Lynn can't make a particular engagement. Listen to me?! I'm already lining up the marketing and PR shoots. Ah well, I am thinking successful thoughts and working hard to fulfil the vision. Web Site Design Shelly Ferner is refining the visual design for our web site and coding a CSS file for us. The current prototype is really shaping up. We will also need a little PHP programming to get that exact look and feel. Our volunteer developers will need to do that for us.

Future Action Items

Beta Project My aggressive goal is to have a working beta by the first week of November. I need to set your expectations though - deadlines are much tougher to hit with volunteers than with dedicated employees. Regardless, I need a target date to shoot for. Specific tasks to be done as part of this objective:

  1. Write and verify the roles and processes of the medical research process discussed with Dr. Marti-Renom.
  2. Write and verify the beta conceptual design with community roles and use cases defined.
  3. Discuss the roles, processes and beta conceptual design with the developers.
  4. Work with the developers to deploy one to three examples using open source software.
  5. Get feedback from Dr. Marti-Renom and modify as necessary.
  6. Give userids to a few medical researchers that Dr. Marti-Renom is working with on TDI's first collaborative project.

Incorporation Process One of the things I did in California was spend some time talking with several other non-profit organization leaders. The amount of time required for organizational overhead and fundraising was quite intimidating. I was advised to look into avenues of being folded into other larger organizations that have goals aligned with us. My anxiety with pursuing this path is that I could spend six months looking for that organization and not find one and then have to incorporate anyway, waiting another six months for our non-profit status. Therefore, I hope to parallel path this. Kara plan to meet with a non-profit lawyer soon to ensure this is possible and if so to begin the incorporation process. Web Site Design Once Shelly Ferner is through with the style sheets we need one of the programmers to modify a few PHP programs for us to get the complete look that we want. I'm hopeful that won't take long and that we will have a good looking web site as soon as the end of October. But, the Beta site is higher priority and if we're short on developer capacity our web site will be the one to get delayed; the community prototype comes first. At this juncture, it's quite possible that we'll defer skinning our web site until our community prototype is more solid anyway - perhaps all work will be done with our community software and never with Wordpress. The good news is that with CSS Shelly's work should be largely reusable regardless of the source application generating the HTML. Some of the class and ids may need to be renamed but I'm hopeful this won't be a painful exercise.

General Feelings

I'm extremely pleased with our progress. I feel real traction and a burning desire to be able to do this full time.

gtaylor's picture


Our web site is live!

Big thanks goes to Rich Manalang for taking Shelly Ferner's visual design ideas and creating the style sheets for our Wordpress implementation. I think it's really looking sharp. We still have a few things acting squirrelly depending on what browser you're using and what page of content you're looking at. Randy Akl has jumped in and is starting to fix those one by one. We're getting there! We focused more of our time on getting the pilot site right than we did our own site. Ahh well, our priorities are well placed.

Our pilot research community for malaria is up and live!

Feel free to browse around: But unless you're a working on malaria, I'd rather you not create an account for yourself on that community. If you have something to say on our general mission and objectives, create an account for yourself on our main site and write a posting here. The more people contributing to this site, the better.

Big thanks goes to Ken Pugsley for establishing our backup procedures and development environment. This can give our users peace of mind that their data is safe and gives developers a place to make changes without fear of clobbering the real site.

HUGE thanks goes to all the open source developers at Drupal who gave us such a great platform to start with. We plan to contribute as many enhancements as possible back to the core Drupal codeline so that others can also benefit from our work.

More information about the pilot project can be found on our Malaria Community Status page.

We're incorporated

Yes it's true, I hired a lawyer and filed our articles of incorporation early last week. We still don't have our non-profit status so I'm afraid that means we still can't accept your money. Step by step...

Met with Duke University members of Tropical Disease Initiative

On November 9 I met with Arti Rai, Tom Kepler and Lindsay Cowel at Duke University. The meeting was largely an introductory meeting to better understand each others talents and commitment. For example, Tom personally knows Jessica Kissinger, the lady in charge of PlasmoDB, an online genome database for Malaria and will work to ensure that our effort is collaborative, and not competitive to her existing efforts.

Arti is a professor of Law at Duke specializing in patent laws and the biopharmaceutical industry. Arti is quite committed to finding a path for open source scientific research to work. She's a founding member of the Tropical Disease Initiative and has authored and co-authored several published papers on the topic. Arti has also indicated that she's willing to help pound the pavement to get our efforts funded as well as serve on our board of directors. Having a boardmember with Arti's expertise on the biopharmaceutical industry and patent laws will be critical to our success.

Wrote Basic Collateral for Our Pilot

I added a web page to our site just for our pilot status. I also wrote a one page introductory one page flyer to describe who we are and what we're doing. Those of you who have worked with me closely know that I struggle to keep my messaging appropriate for an external audience. I tend to be in the project details too much. I therefore had our marketing advisors give quick turn around feedback on the flyer. Thanks goes to Lydia and Paul for that feedback. I think Paul would have me tone down more of the jargon and I may still make another round of edits. Feel free to send more thoughts on the subject now that you've seen the second version.

Future Action Items

Open house at UCSF

UCSF is holding a building innauguration for their new Mission Bay building on November 28. I visited the building during my last trip to San Francisco and it's beautiful. The event is held to demonstrate their new potential to future grant givers. The Computational Biology department has decided that the Tropical Disease Initiative will be interesting to these people. Therefore, Marc A. Marti-Renom is going to set up a poster as well as workstation to describe our jointly developed pilot malaria community. I've seen a copy of the poster and Marc did a fabulous job. It looks very professional. Our web site name is mentioned quite prominantly and there's a screen shot of the community too. Marc has also agreed to have a stack of our new one page flyers about The Synaptic Leap for people to be able to walk away with.

This is a huge opportunity. I only wish that I could be there to talk to people and hear their reactions to our project.

Fill Out IRS form for non profit status

Ok, I'm going to pre-complain here. According to my lawyer, this is a 28 page form with 38 pages of instructions. And according to my Non-Profit for Dummies book, they say it asks brilliant questions like - "do you plan to operate like an opera?" I've contacted an accountant and they said the best thing for me to do is to take a stab at it and then bring it to them to discuss in detail. Uggh. I'll be lucky if this is done by Christmas.

Support the Malaria Community

I've already created a list of tasks and enhancements we need to do for the malaria community. I also need to monitor the site and talk regularly with Marc. Our user feedback will likely reshuffle the priority of those tasks as well as add to the list.

General Feelings

I'm tired. My volunteers are tired. We hussled to get things in shape for the UCSF open house. That's hard to do on the side - especially just before Thanksgiving. Likely our activities for December are going to be light. We simply can't burn out; this is too important. It would be easier to handle if it were our full time job. The issue here is that we're doing this in addition to our full time jobs. We need to get funded so we can do it properly without burning out. To do that we either need to find a fiscal sponsor or get our 501(c)(3) status from the IRS. More time, more work...

gtaylor's picture

Happy holidays! The pilot site has been available for nearly a month and we're already feeling the success. Read on. I hope you'll be as excited as I am.


Marc has been busy promoting our efforts

At the end of November, Dr. Marc A. Marti-Renom introduced the Tropical Disease Initiative and The Synaptic Leap to people at the building inauguration for the California Institute for Quantitative Biomedical Research (aka QB3). He handed out his poster promoting TDI's leadership in our pilot site for Malaria and also passed out the one page flyer for The Synaptic Leap. A week later Marc gave a presentation to scientists at the QB3 neglected diseases symposium. During the presentation he described TDI and TSL objectives and also described his first few projects for the community. I've been quite impressed, envious even, with Marc's visual design appeal of both his poster and his presentation slides. He's more than just a computational biologist (as if that weren't enough...).

Marc has built a social genomics collaborative module

Marc has built a tool that will allow scientists to prioritize and discuss genes for scientific study. It's up and working in our development site now and is being tested for migration to the pilot community. Think of it as delicious, with scientific comments and geared for genomics. If you want more details, you can check out his presentation. I can't thank Marc enough for his contributions. I truly think that projects such as Marc's will be the secret sauce for scientific collaboration and I hope that his project will inspire future scientific collaborative modules.

Others are noticing

Marc's promotional efforts are paying off. On December 16, Jamais Cascio somehow heard about us and posted an article on World Changing. World Changing is well read by online standards and is showing up as syndication on other sites such as Salon Blogs and the Daily Glyph . There's also a brief blurb about us on Smart Mobs. According to Technorati, those sites have spawned about 1,800 links about The Synaptic Leap. As the word spreads we're getting more visitors on our pilot site e.g. yesterday our concurrent visitor count was hanging around the mid 20's and peaked around 30. I must admit that's more than I was planning for at this early stage and feel that we're still looking quite rough around the edges for that much traffic.

Scientists want to participate

Some of the visitors on the site are scientists ready to pitch in and participate. THIS IS THE CRITICAL ACHIEVEMENT! We have people interested in furthering Malaria research (more on that in the next status note as it firms up) and Mat Todd at the University of Sydney wants to start a new community for Schistosomiasis. Schisto is another tropical disease that afflicts approximately 200 million people. Mat's description of the first project:

Essentially the drug used to treat schisto is good, but the synthesis of it needs a big improvement. At the last conference I was at, the WHO people were clear that the improvement would be desirable. I have a plan for addressing this, and think it would make an excellent trial as the first open-source project in organic chemistry.

This is awesome! Schisto is another high priority disease of interest with Tropical Disease Initiative and I'm quite happy to have another community as well as another active area of research discipline (organic chemistry). My future vision is that our site will help scientists across the research disciplines to make connections and to find the cures. The exciting challenge will be to provide the appropriate tools for these cross-discipline scientists with very different research methods.

Getting pilot community feedback

Our community is still quite raw with a goal of finding the critical things to change before launch. Ok so the cat may be out of the bag already. Hopefully people will be foregiving as we tighten things up. Professor Stephen Maurer (TDI) has provided some very good insights on areas for improvement and I've been able to address a few of them, but have many more to go. I'm logging each issue I find as well as those that others send me within a database for ranking, prioritization and delegation. Thanks Stephen for your input and by all means, keep them coming!

Future Action Items

Looks like we're getting more attention than I was really ready for at this stage. I'm feeling quite exposed on our vulnerabilities. I'm going to take about two weeks off my Oracle job to tighten things up. Specific objectives below:

Add Schisto community to the pilot

The pilot will no longer just be for Malaria. Therefore, I need to re-brand and reorganize our navigational structure so that we can add a second community for Schisto. I already have a draft of this up in our development site, but need to tweak it some more and get confirmation from our Malaria community that the changes are good.

Prioritize pilot feedback for enhancements

As we've had some minor usage with our pilot community, we've been getting feedback on need for improvements. Some can be modified with different configuration settings and they will be the first to be addressed. Other feedback items need to be prioritized and requirements need to be refined. I want to get this in a state that I can delegate the work that needs to be done to make the site rock solid.

Roll out Marc's scientific collaborative tool

Marc spent a lot of time on Tropical Disease Initiative this past month and now must focus on little things like grant proposals. What the guy wants to get paid or something?? :-) Once he comes up for air on that, he plans to write appropriate introductory information and to roll out a v1 of his new genomics collaborative module to the pilot community.

Get us in a state where we can accept donations

I need to fill out my IRS paper work so that we can begin qualifying for our 501(c)(3) status. Yes, this was on my list last month. But Malaria community support was higher priority and took more time than I expected. Regardless, this must get done. I'm also looking for potential organizations for fiscal sponsorship. One of our advisors, Cindy Sisson, is arranging a lunch with a contact she has at The Foundation For the Carolinas. I also have a few other angles to pursue.

Create a launch plan

It's time to organize our message and activities for an official launch. Our (current) target date is February 3. Scott, Stephen and Arti have agreed to help with the first meeting over the holidays. After that I will pull in a few others.

General Feelings

I'm excited beyond belief. But I'm also scared. Have I waited too long to promote this? Did we do it on too much of a shoe-string budget? Will folks be forgiving on the things that aren't perfect? I have to take a deep breath and remind myself this is a world changing marathon. As long we work to empower the scientists and allow them to drive this site and build enhancement modules, then I think we will succeed. The buzz on the net will only get louder which in turn will drive more traffic and hopefully have more scientists plug into the community to find those cures. My focus: we're to provide the online platform to serve the needs of open scientific collaboration; scientists are the key to the cures. If we can keep that in perspective in all that we do, then I believe success is just a matter of hard work and time.