Welcome! I'm Ginger Taylor and am the leader for this general open research community within The Synaptic Leap. The general community is a place to discuss general topics on what we need to do to make open source biomedical research successful.
As a guest on The Synaptic Leap, you can browse and look all you want. You must login and create a user profile for yourself if you want to participate. Once you are logged in you may begin collaborating with other community members and become a part of the collective intelligence trying to make open source biomedical research a reality.
See current projects for a list of our active open research projects. You may learn more about these projects and learn how you can participate. At present, these mostly center around projects to enhance The Synaptic Leap web community. However, any non-disease specific project furthering the concept of open source biomedical research is encouraged to create a new project page by creating a child page within the current projects document.
If you're still in the brainstorming phase of starting a project, write a blog article to discuss your ideas with other TSL community members. Working together, we can direct the research towards the most promising ideas.
You can also help shape and direct other open research ideas by reading and commenting on other community posts.
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.
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.
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.
UsefulChem Project is a blog focused on chemistry.
I encourage you to add comments below to list your favorite collaborative scientific website or tool.
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.
This is still at the idea stage so far. Once I write down the requirements, I will attach them to this project page.
I need at least one software programmer with the following skills:
If you're interested in potentially helping out, login and post a comment below. If you have further questions, email email@example.com.
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.
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): Î´ 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) Î½max/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.
The project is temporarily suspended.