Current General Open Source Research Projects

All general (non-disease specific) open source research projects currently in process should be created as child pages to this page.  See the "add child" link at the bottom to create your own project page.

Changes to Support Multiple Research Communities


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. 
  • Remove the TinyMCE editor (format tool similar to ms word) from the user profile pages and expand the box height so that it's never too small to use.
  • Clean up the main content area of the front-page.  We need one welcome page to introduce people to The Synaptic Leap.  More detailed community and posts should be published within those communities.
  • Create community welcome pages introducing the community leader and information about the disease.
  • The left-hand navigation is to support multiple communities, needs to surface a recent posts link,  end-user specific links such as my subscriptions, and a link to our IP Policy that Arti Rai is writing for us. 
  • Provide community specific navigation folders for research projects, research tools, RSS News feeds, discussion forum, Posts... 
  • Matthew Todd, our new schisto community leader, has requested that we create blocks for aggregated news feeds for malaria and schisto and keep them in the left-collumn.  He feels that this is a significant benefit for our users and that a summary should always be visible  and more details available within the communities.  Hopefully this will also help to draw users into the research communities.
  • Create a link for recent posts in the left-hand navigation menu and put it at the top of the menu.  This link will let users quickly explore where recent new posts have been made regardless of which community they were posted in.
  • Add new content attributes for Community and Subject so that users can publish their posts into the appropriate community and within a consistent category within that community.
  • Use the "book" module to organize research projects and make it easy for any member to edit and create new book pages and revisions.  Think of it as wiki, with a built in table of contents hierarchy.
  • Enhance member profiles so that they can associate themselves to a particular research community and therefore be discoverable by other registered users within that community.  NOTE:  a person must have an account to see any user profile, this is not publicly displayed.
  • The right-hand navigation is to become a member center, with blocks to support login, who's logged in, who's new, members directory, and a privacy policy link.  Again, only those logged in can drill and see the profiles. 
    • Our community leaders requested the who's new block.  However, one of our web advisors has said that it can feel invasive and may deter people from registering.  Therefore, I've decided to make this block optional, with the default of off.  This means that a user must register first and actively turn it on.  If others feel strongly we should change it back to being defaulted on, let me know.  It's a simple check-box configuration thing.
    • I'm also going to add a block for recent comments on the right.  This will allow users to quickly find and drill to where the current community activity is.  Although the side collumns are getting rather busy, I have already found this enhancement to be quite helpful in our development environment.
  • Create a getting started book that will serve as "Your Guide to The Synaptic Leap".  This will take time to complete. 
  • Simplify the discussion forums.  Although Drupal supports hierarchical forums we simply don't have enough activity to support more than one forum.  We can always add more later.
  • Re-brand the header and the footer to The Synaptic Leap - The malaria research community will exist within The Synaptic Leap.
  • Have the search box visible and stay put at the top of the left-hand side.  
  • Add a google scholar search box on the right side. It will default as on; registered users can opt to remove this block. 

Longer Term Changes 

  • Add Marc's collaborative genomic ranking and collaboration tool
  • Implement Drupal's freelinking feature to provide the wiki feature of being able to create site documents from a link added to a page.
  • Make it easy for a user to draft several versions of a blog before publishing it.
  • Enhance the editing tool to support more formats e.g. blockquote, citations and more - but not too many :-)
  • Create a simplified process to allow authorized scientists to build new scientifically-specific collaborative modules for The Synaptic Leap.  I will write a requirements document for this first and solicit feedback before we build it.  
  • Add a push-button module to allow new communities to be created by scientists willing to lead a new research community.
  • Update our stylesheets to support good-looking print documents.  Have you printed anything from our site yet?  Not very pretty.
  • Add the captcha module to keep non-human spammers from logging on and making bogus postings.  Fortunately this isn't an issue yet.
  • Improve the image integration within a post.  It's very clunky.
  • Add spell check.
  • Add a Terms of Use check box as part of the registration process.  Sorry to get so administrative on you.  However, we think it's important that people see our guidelines for posting information.  We'll likely include copyright and patent guidelines as well as our privacy policy.  I'm working with our legal advisors and hope to persuade them to minimize the legal jargon and keep our intentions clear. 

Potential Longer Term Changes (let us know if these are desirable or not) 

  • Add a project tasks module to help project participants communicate action items and due dates
  • Provide the ability for users who are logged on to IM each other - must support the ability for an individual user to turn this feature off.

Common Scientific Research Tools

Collaborative Drug Discovery's web-database enables scientists to archive, mine, and collaborate to more effectively develop new drug candidates for commercial and humanitarian markets. 

OpenWetWare is a great site for scientific wikis.  You can create wiki spaces to suit your needs. We hope that all wet lab scientists in our community reference and contribute to that wiki as they work on their open research projects within TSL. 

Connotea and CiteULike are social bookmarking sites specializing in academic content. They also produce RSS feeds! 

UsefulChem Project is a blog focused on chemistry. 

I encourage you to add comments below to list your favorite collaborative scientific website or tool. 

Scalable Development Environment


general open research

Project Description 

Marc's collaborative genomic modules for malaria have inspired me.  Given the power of open source solutions such as Drupal, any community savvy software person can deploy a collaborative community.  The secret sauce is allowing scientists to help extend the collaboration modules to meet new and yet-to-be imagined needs.  My goal is to provide a push-button software development environment for other programming savvy scientists.  We need to provide secure access to the development tools, complete with development standards and guidelines, version control, quality checks and migration to the main site procedures.  These same tools will enable us to put any volunteer to work in evolving our platform. 

Project Status

This is still at the idea stage so far.  Once I write down the requirements, I will attach them to this project page. 

Project Participants Onboard

  • Ginger Taylor - requirements analyis
  • Doug Chasman - programming and environment configuration
  • Chris Heller - will provide a little trac and subversion guidance and will assist with migrating our current trac implementation to another hosted environment. 

TSL Programmers Needed


Request for Help


general open research

I need at least one software programmer with the following skills:

  • PHP programmer
  • Unix shell scripts
  • MySql administration experience
  • System administration experience with development and production environments, backup/restore...
  • Familiarity with Drupal a strong plus
  • Familiarity with Trac a strong plus
  • Familiarity with Subversion a strong plus

If you're interested in potentially helping out, login and post a comment below. If you have further questions, email


Project overview

Trial Synthetic Procedure for Chemspider to Find...


general open research

There has been an interesting conversation over at Friendfeed about the value of centralised vs. decentralised synthetic procedures for chemistry. i.e. should we try to create a store of chemical reactions, or ought we to be expecting decent search tools to be able to find these for us, wherever they are. From my perspective, both have value. Naturally what we need are tools that understand descriptions of reactions that are semantic (plain English), and which can understand various forms of data that go along with compounds.

So I thought we'd give it a try with a random sample procedure, the conversion of tetrahydroisoquinoline to its Boc-protected form. Below is a simple procedure for this, written as if we were submitting this to some web archive of procedures. Also attached are some data for the product - .dx files for JSpecView-ing the proton NMR spectrum, plus a pdf of the same. There are gifs of the reaction itself, plus one of a TLC of the reaction. I'll shortly upload some other things below. I have no idea what any search tool will make of such a mish-mash.

Antony Williams can hopefully unleash ChemSpider, and extract information from this? I also want to try to upload the same data directly to the relevant page on Chemspider, to see if I can just deposit it there. Which of these two approaches is preferable?




Submitted by Althea Tsang and Matthew H. Todd, School of Chemistry, University of Sydney, NSW 2006, Australia. Checked by Victor Sun, Lakshmi Raj Baratha, Soo-Jean Park, same address.



Preparation of Boc-THIQ


To 1,2,3,4-tetrahydroisoquinoline (2.00 g, 15.0 mmol) in dichloromethane (10 mL), triethylamine (3.1 mL, 22.6 mmol, 1.5 eq) and 4-dimethylaminopyridine (0.180 g, 1.5 mmol, 0.1 eq) were added. Di-tert-butyl dicarbonate (4.92 g, 22.6 mmol, 1.5 eq) was added and the reaction mixture stirred at rt for 24 h. The reaction mixture was diluted with dichloromethane (50 mL), washed with water (50 mL) and the organic portions extracted, dried (MgSO4) and concentratedin vacuoto give a bright yellow oil, which was purified by flash column chromatography (3:1 ethyl acetate:hexane) to give the product as a bright yellow oil (3.49 g, 99%)


TLC (hexane:ethyl acetate, 5:1) after 3.5 hours indicated only product and baseline spots. TLC after 23 h indicated slight appearance of second spot at Rf = 0.38.




1H NMR (CDCl3): δ 1.49 (9H, s, H9), 2.83 (2H, dd,J5.8, 5.8, H4), 3.64 (2H, dd,J5.8, 5.8, H3), 4.57 (2H, s, H1), 7.05 “ 7.35 (4H, m). IR (CHCl3) νmax/cm-11682, 1419, 1173. m/z (ESI) 132.1 (100%).


Reference: Reductive deprotection of allyl, benzyl and sulfonyl substituted alcohols, amines and amides using a naphthalene-catalyzed lithiation, E. Alonso, D. J. Ramon and M. Yus,Tetrahedron1997,53, 14355-14368.




1) Original procedure used 1 N HCl wash as well as sat. NaHCO3 wash. No column chromatography.
2) Dilute NaHCO3 wash used in above procedure, working equally well.
3) Column in 1:1 hexane:ethyl acetate works equally well.




general open research

The project is temporarily suspended.