A collaborative effort to create free tools for Gene Expression Profiling analyses. AppleScript and Apple centered project.

Contacts: and Credits: ###

Introduction

One may be able to carry the human or bovine genome in his iPod, but this is not enough. Despite the fact that a large variety of tools were made available by the NCBI to Mac users, those remain essentially classic tools, developed for genetics. That is to say, not quite fitting the specific needs of genomics and almost without interest for pharmaco-genomics.

Existing tools need to be carried to the Mac platform and new ones must be developed in order to help scientists in this relatively new domain. They could (should?) be freely distributed tools, developed by Mac Users as a gift to the scientific community.

Applescript may be a first approach. Let’s have a look.

So What is This About?

There is clearly a need for new tools in the field of pharmacogenomics. In my daily practice I had to invent new ways to manage information available from public databases and/or issued by RT-PCR and microarrays experiments, in order to present it in a comprehensive way. Most of my colleagues are highly competent biologists or physicians (sometimes both) but they aren’t always computer litterate. Browsing and word processing often seem to be a limit beyond which many of them will not venture.

Designing and using new tools for visual presentation of the data was a clear improvement in the way scientists were able to use their computer. Let computers compute, leaving us free to think about Science, seemed to be the prevalent feeling.

I am clearly not the guy to write the scripts they need. I create and use my own, to suit my particular necessities, but they remain rough and rather unsophisticated instruments, somewhat akin to silex knives. Altough efficient, they are not designed with neophytes in mind, nor are they up to the standards one has come to expect from a Mac application. Furthermore, I quite simply lack the necessary time to build something ready for distribution, that colleagues might benefit from.

Bottom to Top is done. Top to Bottom is to be done.

Applescripters (of almost any level) ) and IT professionals wishing to help are needed. Molecular biologists with new problems to solve, are welcome.

Participation

Medium to strong skilled scripters essentially, please. I am a newbie and I already have problems to stand myself ;-) But everybody will have access to the blueprints of the projects as they will be made available online. And comments and new ideas will be welcome from anybody interested by the project. Today's newbie will be tomorrow's power scripter anyway. If you think you are able to help, please do so.

Everything contributed is to be free for anyone wishing to use it, under a Creative Commons license.

Attribution is mandatory, so we know whom we have to thank for the work. Eventually for him to be identified as a potential collaborator by people seeking bioinformaticians for their staff.

Non-Commercial is essential. No money making from benevolent work.

Share Alike is a wish, as I don't think we will have the ability to track that.

And this is the license coming from Creative Commons:

Creative Commons License
This work is licensed under a Creative Commons License.

Benefits

Why participate? For the pleasure to help science battle against genetic diseases, for recognition from Mac users, perhaps future collaborators.

And for fun. This is a collaborative effort between friendly people. Most Mac users I meet are friendly and wishing to help each other. And always find a way to have fun while doing so. I don't see any reason why history should not repeat itself once more.

Think about it, the different way.

Requirements

We would like to see as many GeneScripts as possible. Droplets, mini-applications, Applescript Studio productions. GeneScripts is about helpful tools that may improve every day's life for scientists trying to improve our lives. Two main qualities for GeneScripts: ease of use and efficiency.

Antoine will provide some basic projects to realize, most of them with bits of scripts already functional. But probably highly improvable. Workflows for the final scripts will be presented as OmniGraffle diagrams. Attaching scripts to forms always was helpful to check the different steps of an application during the analysis steps.

Thierry will supervise the evolution of each project. Management from a non-biologist, used to carry out software development projects seems interesting. And he is the ideal beta-tester. If he can manage to use GeneScripts (and get the results right), without having to ask any further questions about how it works, that will be a good omen about the usability of the script and the quality of the included Help documents.

People wishing to manage one or several projects, coordinate the development steps, beta-test releases as they will be available, are welcome. Before proposing your help, please be sure to be able to do the job.

Biologists from all horizons can submit specific problems, and eventually the ways they think we should handle them. We will try to find solutions and script them. But no guarantees about that. You have nothing to lose anyway. Clearly formulating a problem before submitting it will lead to a better understanding. And public exposure will increase chances even to find an existing solution.