general open research

general content regarding open source biomedical research

02 Aug

Community developer paid position available at OpenWetWare, MIT

Published by rpshetty

Community 

general open research

Subject 

Request for Help

Do you want to change the future of biological research? Are you
looking for a unique opportunity to empower researchers to openly share
information? OpenWetWare is a community of thousands of researchers
from around the world who freely share their ideas, results, tools, and
wisdom. Our project has largely been volunteer driven to date; we are
now looking to hire a full time employee.

08 Jun

New Bioinformaticist, waiting for orders! :)

Published by dalloliogm

Community 

general open research

Subject 

Miscellaneous

Hi!

My name is Giovanni and I'm a student fo bioinformatics, from Italy.

I'm interested in contributing to the synaptic leap. I've noticed that this website isn't seeing too much activity lately, and I'm sorry for that, but I do believe that the idea of a Scientific Community inspired by the OpenSource one is very good.

10 Apr

Forum on Community-Based Approach to Neglected Infectious Disease Research

Published by gtaylor

Community 

general open research

Subject 

External News

Barry Bunin, a registered user here at TSL and CEO of CDD, is presenting at the upcoming BioScience Forum on April 18. If you're in the SF Bay area, it looks like an interesting meeting to attend.

09 Apr

Open Science Particpation Incentive

Published by IanTaylor

Community 

general open research

I've been following and participating in the Open Science community for a while now. It's ironic, but I suffer from the same tendencies that Ginger (synapticleap.org founder) mentions in the most recent discussion "If you build it will they come". I too have emailed with praise of her efforts, but did not post. I'm not nearly as accomplished a scientist as some of the participants here, but do realize every effort counts. However, still I did not post. So this is my first post with some my observations about Open Science.

21 Mar

If you build it, will they come?

Published by bartrum

Community 

general open research

Hats Off! to Ginger for creating TSL.

I was quite excited when I first found TSL. I was, in fact, looking for an open research community, without much luck. I was actually planning on building a similar website, if I couldn't find one already in existence.

I must admit that I am somewhat discouraged that TSL has been around for over a year, had some rather high powered publicity at kickoff, but seems to be languishing.

Why are not more people here?

What are the issues that prevent people from contributing?

Google Summer of Code 2007

Published by gtaylor on 20 March 2007 - 4:34pm

Google is now accepting student applications for their 2007 Summer of Code program. I think we can leverage this program to get scientific collaborative enhancements added to The Synaptic Leap to take our collaboration for tropical diseases to the next level.

BackgroundÂ

The Synaptic Leap uses Drupal for our website application. It is an open source PHP/MySql solution designed for optional extension/plugin modules. Historically, google has sponsored quite a few drupal extension module projects in their summer of code program. As such there's advice at the Drupal site on how to go about getting your project approved. Â

Subject 

Request for Help

Community 

general open research
10 Jan

Discussion on Ethical Pharmaceuticals

Published by MatTodd

Community 

general open research

Subject 

Miscellaneous

There was a report in a UK paper recently about an 'ethical pharmaceutical' approach to the production of new drugs, by the development of a patent-beating formulation of an existing compound. A discussion just started about this over here.

Mat

 

09 Jan

Open Source/Access Conference

Published by MatTodd

Community 

general open research

Subject 

Miscellaneous

A conference on open access/public knowledge projects is being held in Vancouver in July:

 http://ocs.sfu.ca/pkp2007/

It's interesting that this area has become large/mainstream enough that whole conferences are being devoted to it.

Mat

07 Jan

Collaborative Drug Discovery UCSF/QB3-Hosted First Annual Community Users Meeting Agenda

Published by BarryBunin

Subject 

External News

Dear TSL Members,

 

You are invited to the first annual QB3-UCSF-CDD developing world disease research community meeting scheduled for March 5th 2007 at the UCSF Mission Bay Campus (details below and attached).  The collaborative community includes leading experts on developing world infectious disease research from Stanford, UCSF, UC Berkeley, UCLA, UW, SBRI, St. Jude CRH, U. Penn, Univ. of Sydney, and industry too.  

 

Collaborative Drug Discovery
First Annual Community Meeting

 

Monday, March 5th 2007 1:00-6:00 pm; Auditorium: J. David Gladstone Institute (1st Floor)

Hosted by Gladstone Institute and QB3 at the UCSF, Mission Bay Campus

Two major themes of this event are:

1)      Public-Private-Partnerships for Global Health Issues
2)      “Open” concepts for Collaborative Drug Discovery

Confirmed Speakers:
 

  • Dr. Christopher Lipinski, Pfizer, retired. (Keynote presentation)
  • Jim McKerrow, Professor, Dept. of Pathology, QB3 - UCSF
  • Matt Bogyo, Professor, Dept. of Pathology, Stanford Medical School
  • Andrej Sali, Professor, Dept of Biopharmaceutical Sciences, QB3 - UCSF
  • Dr. Anang Shelat, St. Jude Children’s Research Hospital
  • David Roos, Biology Professor, Univ. of Penn tentatively confirmed (Director, Penn Genomics Institute).

Symposium – Coffee/Snacks – Demos – Posters – Networking – Wine Reception

Registration is free. To register contact/RSVP to: kgregory@collaborativedrug.com.

Histone acetyltransferase inhibitors

Published by wjsullivan on 1 December 2006 - 8:30pm

Subject 

Request for Help

Histone acetyltransferases (HATs) and HAT inhibitors
The significance of studying HATs is underscored by an abundance of genetic studies that implicate them in having a role in disease (for reviews, see (10), (6), and (16)).  Consistent with this, some histone deacetylase (HDAC) inhibitors display anti-tumor activity and are being evaluated in clinical trials (8).  In addition to regulating transcription, HATs have crucial functions in modulating other DNA processes (7).  Histone acetylation machinery may also be a viable target for novel anti-infectives (5).
The impact of the various HATs on cellular physiology and disease would greatly benefit from the identification of specific pharmacological inhibitors, but very few have been described to date (11).  Two natural products, anacardic acid and garcinol (a polyprenylated benzophenone), are reported to inhibit both p300/CBP and PCAF in a 5-10 mM range in vitro (1, 2).  In contrast, curcumin displays activity against p300/CBP, but not PCAF (3).  Subsequent studies suggest that anacardic acid may be a broad-spectrum HAT inhibitor, as it also interferes with the MYST HAT Tip60 (13).  Isothiazolones were identified in a high-throughput screen as inhibitors of PCAF and p300 (12), but like the aforementioned compounds, activity against GCN5 was not determined.  Moreover, isothiazolones are strongly reactive with thiol groups and hence are likely to have substantial nonspecific effects.  Two small molecule inhibitors of GCN5 that have been documented include a butyrolactone (4) and MC1626 (2-methyl-3-carbethoxyquinoline) (9).  However, in our hands, the butyrolactone and MC1626 exhibit no inhibition of recombinant yeast GCN5 in a standard in vitro HAT assay (Sullivan, unpublished).  As a positive control, parallel HAT assays showed anacardic acid does inhibit yeast GCN5.
Two reports describe systems that can be used in high-throughput format to identify potential HAT inhibitors (14, 15).
We are interested in acquiring HAT inhibitors, especially those that appear to be selective for distinct types of HATs (i.e. GCN5, MYST).  Not only would these serve as valuable probes to study histone acetylation in eukaryotic cells, they may also hold promise as novel drugs to combat parasitic disease.
References

 

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