general open research

general content regarding open source biomedical research

10 Feb

TSL Status February 10, 2006

Published by gtaylor

Community 

general open research

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

Accomplishments

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

Community 

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

Community 

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...

Scalable Development Environment

Published by gtaylor on 29 January 2006 - 1:12pm

Community 

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. 
13 Jan

News sources for TSL

Published by gtaylor

Community 

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.

Criteria

  • 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

Community 

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. 

what's necessary before official launch?

Published by gtaylor on 2 December 2005 - 1:11pm

The community is open for full usage.  However, we should have a "launch" date that we announce to others as being a push to spread the word and get others to use it.
Why the hold off on launching?  It is very important that people get a positive first impression.  The site needs to provide an effective "service" for people to come back.  

We need to prioritize the issues that must be fixed/enhanced before the launch date.  To do this, we must use the site and find out what isn't working for us. 

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general open research

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appropriate copyrights for the community

Published by gtaylor on 1 December 2005 - 1:41am
We're now in the embryonic stages of the community.  At this juncture, we have no copyright notifications on the site.  I'd like advice on what is appropriate for our goals.   Open Wetware is using a Creative Commons logo in their footer.  Here's a link to their copyright wording.  PLoS on the otherhand only has a copyright footer showing up on the article pages themselves.

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general open research

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