Your Guide to Using The Synaptic Leap


This book is your guide to using The Synaptic Leap.  It should evolve with the community tools.  Please help us to keep it up to date by either posting suggestions via comments to a page or by creating child pages and hooking them into the hierarchy. 

Comments and new pages functionality are links at the bottom of the page available to all users who are logged in.  We require that you login before making any post so that you can be recognized for your contributions.

Format of the User's Guide 

The User's Guide is created using the book module within Drupal, the open source software running this web site.  Books allow content to be created and maintained on separate pages and then organized hierarchically.  Community participants can easily create child pages to a given page.  User's can navigate the hierarchy using the next and previous links at the bottom of the page as well as the book navigational links that will appear in the upper left-hand corner when a user is browsing a book page. 

A highly desirable feature of books is that at any level of the hierarchy a user can click the printer friendly version link at the bottom of the page and see the entire document from that page downwards, expanded and in a web page format without any TSL web site features such as header or navigational menus. 

As you begin to dive deeper into our research communities, you will notice that our research projects are also maintained with the book module.

Login - Where and Why

The login link is in the upper right corner of The Synaptic Leap. Before you login you are a Guest. We encourage you to create an account, login and become an active member of The Synaptic Leap. It's free! The following page describes the features available to both Guest and Members of The Synaptic Leap.

Guest users may do the following:

  • read all content including projects, RSS news feeds, research tools pages and more
  • subscribe to various content changes via RSS using the XML button in the bottom left corner

Logged on members may do the following additional things:

  • create a community profile to publish your skills and interests to other research scientists
  • you elect whether other members can contact you you from a profile contact page or not
  • discover other research scientists with similar skills and research interests by using our members page and drilling into author profiles
  • post comments and questions to blog postings and discussion forums
  • subscribe to email notifications for recent activity about a particular post, discussion forum...
  • write and maintain your own blog, publishing it into the various research communities within The Synaptic Leap
  • respond to community polls and have your opinion count
  • create a poll and publish it to the community members for them to answer
  • and lastly and most importantly - participate in an open and collaborative project, maintaining your own project information within the community project book
  • check out the following link for information on our privacy policy

Membership has its privileges. (Sorry, I couldn't resist.) Get off the sidelines, login and get active.

Site Level Email Subscriptions

Configuring Your Subscription

You may choose to have daily email notifications sent to you from The Synaptic Leap. You must have a registered account first. Once you have have registered and are logged in, you can go to your personal user profile and hit the "my notify settings" tab. From there, you just enable the various buttons.

I configured my settings so that I get a headline, teaser and link for all new comments and articles posted on the site.

click the image to see a full size screen shot of

If no new posts are made, no email is sent. If multiple posts are made, you only receive one email summarizing the posts with links to each post. The email that is generated also includes a link back to your personal notification settings so that you can easily disable it anytime should you ever wish to.

Sample Email

Subject: The Synaptic Leap notification for gtaylor
Date: September 10, 2006 5:15:02 AM EDT

Greetings gtaylor,

Recent content

published personal blog entry by gtaylor: Can open-source R&D
reinvigorate drug research - Nature
Bernard Munos, from Eli Lilly, wrote a very thorough article on open
collaborative research for neglected diseases and it was just published
at Nature: Can open-source R&D reinvigorate drug research. What I
particularly like about the article are the details he provides in
describing how he thinks pharmaceutical companies can and should
participate in the process. Let's face it; we're in uncharted
territory. We don't really KNOW how it's going to work. We're in the
midst of a big evolving experimental process.My vision for how it will
work tends to be a bit more grass roots, less centralized group driving
the process. Collaborative process tools like a Gene Wiki (described a
bit in that presentation) will enable dedicated experts to suggest work
for less involved volunteers to contribute. People will collaborate
the people they trust and trust must be earned. The nice thing is
that I firmly believe that both the centralized group idea of Bernard's
vision and my grass roots vision can co-exist peacefully and
occasionally collaborate together. Again, it will be a matter of trust.
Over time, the centralized group may win over the grass roots
contributors and bring them into the fold. Again, it's all a matter of
[ ]

Recent comments

1 new comments attached to: Storing structures and views for search
Molecule Representations by MatTodd

1 new comments attached to: Can open-source R&D reinvigorate drug
research - Nature
Que Sera Sera by MatTodd

This is an automatic mail from The Synaptic Leap
To stop receiving these mails go to

Introduction to Collaborative Communities

The Synaptic Leap communities are generally disease specific.  Our goal is to connect scientists with various research skills working on a particular disease so that they may collaborate together and offer fresh perspectives on the issues at hand. 

During our pilot phase, we are focusing on tropical diseases.  For example, we have a community for malaria and a community for schisto.  You can navigate to these communities by using the navigation folders on the left.  

research community navigational links 

There is also a general community for open source biomedical research  It's the only non-disease oriented community and is intended to be a community for general open and collaborative biomedical research tools, discussions and site postings. 

Each community acts as a mini portal assembling recent research articles, and web-based research tools to study the research community's disease of focus. Users participating in multiple research communities will quickly become familiar with this common infrastructure. The various community tools will each be discussed separately. When you click on a research community navigational link e.g. malaria research, you will be presented with a welcome page in the main content area and the primary community links will expand in the navigational box on the left. 

research community tools navigational links 

Each research community is led by web-savvy scientists studying that disease.  These scientists help to assemble the tools and resources you will need to research and participate in collaborative research projects for that disease.  Thanks to the web, these resources are growing rapidly.  If you know of an important resource that they are missing, pipe up by commenting on the pertinent page or by posting a blog and publishing it to the appropriate collaborative community. 

If you wish to lead another community conducting open, collaborative research projects focusing on another disease, contact Ginger.  

Current Projects

When people and ideas within The Synaptic Leap connect and mature, they blossom into open, collaborative research projects. Project information can be maintained within the Current Projects section of a research community. Projects, like this user's guide, are created using Drupal's book module. Books allow content to be created and maintained on separate pages and then organized hierarchically. Community participants can easily create child pages to a given page. User's can navigate the hierarchy using the next and previous links at the bottom of the page.

  • Projects are listed at the bottom of the main project page.
  • Any user who is logged in may create and describe a new research project by simply adding a "child page".
  • Printer-friendly versions are available for all projects from the main project page, or for a specific project from within the project-specific page.


overview of main current projects page for malaria community


When creating a project page, remember you are publishing the information on the web. You need to make it easy for people to browse and get a good overview of your project with an ability to drill for more details.

Suggested section headings within a project page:

  • "Aim" or "Overview" - 1-2 paragraphs describing the objective of the project
  • "Who's Involved" - gotta give credit where credit is due. We also suggest that you link each name to a bio page or their TSL user profile page.
  • "Status" -
  • More project details perhaps on the page or perhaps attached as ppts/word docs/ excel spreadsheet for issues and to-do tracking... Or you may choose to create multiple child pages of the project page. Use these tools to help you coordinate tasks amongst your project members. The more details you include, the more others in the TSL community may "comment" on to help direct your research efforts. You never know what might have already been tried or who may have a fresh perspective that may offer a critical new insight.

Additionally, we suggest that you create a child page to tell others how they can get involved - donating data, materials, or specific research skills needed. By creating this as a separate page, you can also publish it to the Resources Needed page by simply selecting the Resources Needed subject.

creating a "resources needed" page


Creating Content

There are five primary types of content within The Synaptic Leap:

  • Project Pages, created as "child pages" for research community projects using the book module
  • Personal Blog pages, used for pre-project style brain storming communications

The content publishing applications are your online collaboration tools within The Synaptic Leap. With a few basic concepts down, you'll be ready to start collaborating with your fellow scientists.

The following will describe the common form fields across all content types and how you can use these fields to direct where your content should be published within the TSL site. Content specific fields and instructions will be described in the respective user guide sections.


The title is exactly what it sounds like, the tile of your content. When filling in your title, think about what pages you plan to publish your content on. How should you best describe your content for others to scan the entire web page and quickly know what your piece of content is about.

For example, if the content is going to be published to the Resources Needed page, then you might not want to use the title "Resources Needed" instead, describe more specifically what's needed e.g. 2 computational biologists needed for malaria effort.

The Community field is used to publish content to the appropriate communities within The Synaptic Leap. For example, any content with a community of malaria research will be published on the malaria research community posts page. A post can be published to multiple communities by holding the ctl-key while selecting the appropriate communities.

Sometimes you may not want a post to go to any community posts page. For example, you may create an image which for the sole purpose of referencing it within another piece of content. In cases such as this, it is best to keep the community selection as <none>. Â


subject form fieldÂ

"Subject" represents general subject categories for a piece of content. Later, we may chose to provide navigation for Community/Subject specific topics e.g. a navigation page for General Open Research and Community Status. Â

At this juncture, the only Subject driving content publication placement is the "Resources needed" subject. Any piece of content, regardless of the community selected, given a subject of "Resources needed" will be published on our Resources Needed page.Â





Book/project pages and blogs have a body. This is where you will write your content that will be published as a web page. If you use Windows Explorer or Firefox as your browser, you will have a fairly robust editor available to you. It will give you basic word processing formatting options such as heading styles, bold, italic, underline, bullets... More web-specific formatting tools include links, images and html.

Additionally, each piece of content also allows for related content via:

  • Comments, created as a threaded response to another piece of content
  • Attachments, files uploaded as additional information to the source content

NOTE: more links and content to be added on this subject later. In the mean time, I hope this post is helpful.

Recommended Browsers for The Synaptic Leap


general open research


If you're using a mac, we recommend using Firefox (

If you're using a PC, we recommend either Internet Explorer 6.0+ or Firefox (

Using one of these browsers will allow you to easily create compelling posts on The Synaptic Leap using an editor that is quite similar to a word processor.

screen shot of TinyMCE editor

More Background and a Little Off Subject Rant

Neither Apple's Safari nor older versions of Microsoft's Internet Explorer (IE) can support our editor, TinyMCE. And unfortunately Microsoft doesn't provide IE 6 for macs. Therefore if you're a mac user, Firefox is your best bet.

Of course, you could turn the tables and say that the editor doesn't have code to support those browsers. Certainly that's fair to say of older versions of IE. After all, IE version 5.0 and before were likely available before TinyMCE.

Safari on the other hand, well as much as I love my mac, and I do love my mac, I think Apple ought to dump it. Web application developers struggle to make things work for Safari, Apple just hasn't kept up with all the de-facto web standards. Given the small user base for Safari, it's frequently not worth it for application developers to write code for Sarari specific work arounds.

Apple came out with Safari before Firefox was a presence. Since then, Firefox has gained serious momentum. It's free and it's a damn good browser. The open source developers are doing a good job of keeping it secure and up to date with the latest web developments. In fact, they drove quite a few of them. Due to its strengths, it already has more than twice the market share as Safari does.

Given this change in the marketplace, Apple needs to adjust their browser strategy. I think Apple ought to take half their developers working on Safari and redploy them on Firefox. Then their next "upgrade" for Safari should be to automatically replace it with Firefox. The other half of the programmers should be redeployed on iLife - keeping it leading edge and easy to use. This is their differentiator and I think they should increase their investment and widen their lead in this software space. Trust me, as great as iLife is there's still room for improvement.

And if the Mozilla partnership works out for them for the browser, I think Apple should do the same thing with their Mail. Apple could take 1/2 their mail developers and move them to Thunderbird. Imagine if Thunderbird integrated well with Apple's address book, iTunes, iPhoto... Ahhh, a real mail client on my mac. That would be nice.

Ok enough ranting. I guess the software product manager in me can't help but jump on this soap box.

The Synaptic Leap User Statistics

In case you're interested, the following are a few of our user statistics (according to Awstats) for The Synaptic Leap for May 2006.

  • Unique Visitors 683
  • 3.14 visits / visitor
  • 3.71 pages / visit
  • Approximately 20% of our visitors are on the site for more than 30 minutes.
  • More than 90% come from a direct URL address or a bookmark. This is a big deal.
  • Less than 4% of people find us from a search results page, with Google of course taking the lion's share.
  • We have visitors coming from more than 24 countries, most are from the U.S. with Australia making a good show too.
  • 60% of our users are on Windows; 15% are on Macs; nearly 7 % are on Linux; the rest??
  • We have a near tie for Internet Explorer and Firefox browsers with 38.8% and 38.7% respective usage. 2.8% of our visitors are using Safari. The rest is others and unknown.

Resources Needed

Want to Contribute?

Our Resources Needed page aggregates all posts for volunteer and resources needed for open research projects. These resources may include lab time, materials, CPU cycles computations - whatever is needed to move an open research project forward. If you are interested in a particular project, login and post a comment expressing your interest.

Need Help With Your Project?

To post a request for resources for your own open research project, you may login and create a blog page with a "Subject" of Resources needed and it will automatically be added to this page. If these resources are related to a specific project logged within TSL you can also create/associate the resource request page as a "child page" to your project page. This will allow people to find your resolource request needs from both your project page and the resources needed menu item.

General tips for posting a resources needed page:

  • People generally scan the web, use bullets
  • Provide explicit links to pages where you have more project details should you entice them with your bullets. You can create a project page or a blog page to describe your project.
  • Describe what's in it for the volunteers. What will they learn, how will they help the world, what great contacts will they make?
  • Consider putting your email information directly on the post. I know that they can always post comments to find out more. But I've seen a big hesitancy in doing that. People are far more open with email.


    Request for Help

    Sharing NMR data with jspecview

    MA4-1-11.dx101.17 KB


    Request for Help


    general open research

    The need to share raw NMR data effectively brought up a small technical challenge, and there have been posts about this here and here. Using our transfer hydrogenation result as a random example, we thought we'd try jspecview, and the .dx file is attached to this post. We've been having problems with this, in that the attached is an FID, not the spectrum, and jspecview doesn't like it. Surely an FID is more useful/interesting? Surely it shouldn't matter?
    Secondly jspecview seems to worry about where it's installed - directly on a c: drive is better than elsewhere, we've found. When I did get the program working on a sample spectrum, I couldn't do much beyond look at it and zoom in. I was not able to integrate manually, for example. Can jspecview handle 2D spectra? Any open alternatives for this?
    I'm being a pedant - it's open source and in development. But I worry that if we're hoping organic chemists will adopt this tool more widely, e.g. for the routine analysis of supporting information to get away from pdf'd spectra, we need to greatly reduce our expectations of their computer literacy first.