I recently found a program named ATLAS ti for qualitative analysis, you might wanna check it out

I didn't Know MVC, DRY or others you talk about, Maybe if you need software R is a free and powerfull tool to handle and analyze data.

Thank you very much! I will try to download ATLAS program if i find it.

I just suspected someone already created an efficient way to manage scientific data. I do have sql database for my experiments, but it got a bit cluttered and consumes a lot of time and energy..

Thanks for your insights. I was looking for a programming tool, but ATLAS sounds interesting. I hope it will simplify my data handling. I was also interested in R, but my problem is in organization of data rather than in analysis.

I'm not a biologist and haven't used any of the approaches you mentioned so I can't comment on them although data organization, analysis, and presentation apply to most all of us. With that said, I found J. Scott Long's "The Workflow of Data Analysis Using Stata" to be a fantastic resource in that it explicitly outlines and describes what efficient data workflow looks like and how to do it. The book is, of course, geared toward to Stata users but I suspect the principles would be helpful no matter what program you use.

I suggest using scientific workflow languages/engines to run your experiments, preferably one with provenance management. Vistrails, Taverna and Chiron are examples of these.

I´m sociologist, but usually in social sciences we confront problems with different kinds of data (quali/quanti). I used ATLAS-ti long ago, but droped because is expensive, and a little time-consuming... not fitted for quick tasks, but useful and light. The learning curve is long, if you want to make the very best of it.

Now I use a combination of my own folders-structure/file-naming, and open or free software to visualyze info structure: Cmaptools (http://cmap.ihmc.us/) and its ontology management version COE (http://www.ihmc.us/groups/coe/); or now I´m using Docear (http://www.docear.org/), that automaticly creates a mind map of folder structure with links to files... and even to bookmarks if the pdf file has table of contents! (well, if is not protected).

Recently I found a not-so costly option for data organization and analysis as a on-line service: Dedoose (http://www.dedoose.com/).

I hope this helps.

Thanks a lot for your inputs! I was not aware of these tools you guys mentioned, and they might be something I have been looking for. I imagined that our research and data are so diverse that it might be difficult to make a generic tool. But it is nice to know that people have already implemented some software that could make my life easy.

-Nikolay, thanks for sharing your thoughts. I have been discussing that kind of stuff with my friends, but it was vague to me. Thanks for making it explicit. I can imagine how hard you have been working to manage people's data.. Another way to share data effectively might be to use github. Open source and distributed science?? We can share and edit manuals, for example?

I don't use it (yet) so not sure how useful this is - but I am about to begin to explore Data Finder (http://www.andreas-schreiber.net/2008/07/datafinder-a-python-application-for-scientific-data-management/) mainly because I am helping a set of programmers that are trying to create an elab notebook that integrates with the file management system.

@ Constantinescu I use VUE quite a bit, (and love it) but while it is good for some things, I am not sure I would describe it as a good data management system.

In order to provide a diiferent angle to the discussion, let me express my own set of regrets about how hard it is for research data management project developer teams (based at the University Research Office, Library, etc) to reach researchers and to disseminate research data management (RDM) initiatives and opportunities at an institutional level (meaning university or research centre).

There is a large number of ongiong RDM projects at institutional, national, international and discipline-based levels that seem unable to raise awareness about the need for a systematic research data management to be carried out by research groups everywhere. The technical infrastructure is increasingly available (see LabArchives, http://www.labarchives.com/ to add just one additional example to the ones that were already mentioned), the policies are often there as well (for instance the NSF data sharing mandate in the US, see http://blog.datadryad.org/2010/11/15/nsf-policy-on-dissemination-and-sharing-of-research-results/) and the international networks are already collaborating for harmonising the different national approaches (see "Research Data Management: Activities and Challenges" Workshop held last Nov in Bonn by the Knowledge Exchange, http://www.knowledge-exchange.info/Default.aspx?ID=475, with attached report), so everything seems ready for a broad movement towards an accountable research data management activity to flourish. But we need researchers to be aware of those efforts!

Maybe the publishers are actually the most appropriate stakeholders to look upon for getting these initiatives widely disseminated. Some good news came up last week in this regard, see "LabArchives and BioMed Central: a new platform for publishing scientific data" at http://blogs.openaccesscentral.com/blogs/bmcblog/entry/labarchives_and_biomed_central_a

The best option for the question that you do is the following:

1 - Freemind. Allows a map and can you order it to suit the needs and then export it to a document (odt or html..)

2 - Docear. Academic is a very useful suite that combines freemind and JabRef, but you must have a version of PDF viewer installed so you can go by the marks or comments.

http://freemind.sourceforge.net/wiki/index.php/Download

http://www.docear.org/software/download/

http://jabref.sourceforge.net/download.php