Forum: OMICtools - Call for curators
gravatar for arnaud.desfeux
5.5 years ago by
arnaud.desfeux450 wrote:

We have developed OMICtools, a freely workflow for genomic, transcriptomic, proteomic, and metabolomic data analysis. All tools (programs and databases) have been classified by omic technologies (NGS, microarray, PCR, MS, NMR). Schematic workflows with clickable regions are provided for each omic application to guide newcomers.

OMICtools is expected to serve as a useful didactic resource not only for bioinformaticians, but also for experimental researchers and clinicians. An interface has been established to allow anyone to report a problem, write a comment or rate a given website, in an attempt to develop an interactive community.

One year after online kickoff, OMICtools has 1000 daily users from around the world (34% EU, 33% USA and 30% Asia).

In collaboration with the Neuroscience Information Framework (NIF), OMICtools has added a unique Research Resource Identifiers (RRIDs) for each software tool and database (See the Resource Identification Portal).

As a next step in OMICtools content development, we are assembling teams of volunteer curators to review and categorize programs, databases and links to literature, for each specialized field. The amount of time volunteer curators spend on the project is entirely user-guided.

Twenty volunteer curators recently joined us.

The aim of OMICtools is to build a consortium of users who share our desire to provide the scientific community with an educational and full-quality tool related to bioinformatics.

Participants will be associated in the next publication.

We are at your disposal should you require further information.

Thank you for your time and interest. Any comments and feedback are most welcome.

Best regards,


Arnaud Desfeux
OMICtools coordinator

pcr nmr ms ngs forum microarray • 3.0k views
ADD COMMENTlink modified 5.4 years ago by Marco0 • written 5.5 years ago by arnaud.desfeux450

OK,  but what exactly is the buisness model for STATSARRAY LLC

ADD REPLYlink written 5.4 years ago by cdsouthan1.8k

it is on their website:

ADD REPLYlink written 5.4 years ago by Istvan Albert ♦♦ 83k

Dear Christopher,

The business model of STATSARRAY (website) will not work for me. Competition is to large (see Geoff's Bio-Directories) and I didn’t have enough money to have an immediate impact. Furthermore, big pharma have their own team and academic laboratories prefer to do the work themselves.

I have preferred to focus in the development of OMICsearch and OMICtools. 

My business plan is moving :) I would like to develop a business around these free services.



ADD REPLYlink written 5.4 years ago by arnaud.desfeux450
gravatar for Istvan Albert
5.5 years ago by
Istvan Albert ♦♦ 83k
University Park, USA
Istvan Albert ♦♦ 83k wrote:

I think OMICSTools is a great idea and fills an important need. This need is being slowly recognized for example see this:

The NIH Software Discovery Index | We invite your comments

I would recommend reading this resource and adapting OMICSTools to match what their consensus seems to be.

If I may add one comment on the implementation - personally I think your are trying to add too many things into one site. If it is a directory it does not need user comments, nor user reviews - those are very distracting and it is very difficult to ensure high quality content. What I need is one expert opinion of a curator that actually ran the tool and provides genuine insight and comparison to other tools, a recap and guidance. 

IMHO these just take away the main utility and focus of the site.  I would recommend to have links to documentation, original publication, mailing list, support forum etc. As the saying goes: do one thing and do it right.

ADD COMMENTlink modified 5.4 years ago • written 5.5 years ago by Istvan Albert ♦♦ 83k
gravatar for arnaud.desfeux
5.4 years ago by
arnaud.desfeux450 wrote:

Dear Istvan,

Elixir is also working on this need.

Similar tools exist in each category. Which tool to use? We have to guide newcomers. It is very important.

To answer this question:
-an interface has been established to allow anyone to report a problem and rate a given website
-published evaluations of algorithm performance have been added to provide guidance in the choice of programs.
-We are developing a text mining tool to track the number of times a tool has been used by other researchers (see this recent deep search for software citations). 

We agree with you. It is difficult to use our forum. We have to improve the design of OMICtools.

I contacted you 6 months ago before implementing the forum. We would have preferred to do a link toward Biostars for each tool:)

It would be a pleasure to collaborate with Biostars.




ADD COMMENTlink written 5.4 years ago by arnaud.desfeux450
gravatar for Marco
5.4 years ago by
Marco0 wrote:

I agree with Arnaud. The community needs a tool that not only identifies the various existing softwares, but also highlights the best. But it is always a subjective opinion. That is why the rating system I think is a very good idea. 
Is it necessary to have to list the obsolete software? I'm not on. 

The idea of ​​the forum for each tool is also very good, as well as to associate a tutorial on each tool. This is where OMICTools complements Biostars!

ADD COMMENTlink written 5.4 years ago by Marco0
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