A few words of appreciation for an open source software that can help you a lot in your work, Engauge Digitizer (ED) from Mark Mitchell. ED is a simple, straightforward curve digitizer: it takes images with graphs like the one below and transform them (with a little help) in data you can use later on.
I discover new things everyday … I wrote earlier that I really liked Zotero, a reference management software. However, there is one thing that was missing, imho: the capability to import PDFs (individually or in bulk) and correctly fill in the various fields of the reference. But in fact, this already exists in Zotero! Just drag a PDF in the middle section (the reference list) then right-click on it and choose “Retrieve Metadata from PDF” (*). Retrieval of the title, the authors, the journal, etc. everything goes very fast and they are stored as a normal reference, now on the right. ...
For my work I need to reference a lot of statements, mainly with papers and books in the biological / medical literature. Usually “professionals” use two proprietary software, Reference Manager or EndNote (both owned by Thomson Reuters). But there are a few very interesting free alternatives (see this comparison of reference management software). I switched from Mendeley to Zotero a few weeks ago and I’m very happy. Here is why …
When I studied biology as well as when I did my Ph.D., our professors were always after us because of references. I think with their precious help we learnt the art of referencing: choosing good references, citing them at the appropriate location in a text and, of course, giving enough information at the bottom of the text to allow the reader to find these references. I just finished reading two articles in a recent edition of The Economist and they reminded me how important are these references. These articles are What would Jesus hack? and Worrying about wireless. ...
In software development (as in many other fields, like paper or thesis writing ;-)), you often need a revision control software to effectively manage all the changes made to your source code (or sections and chapters). It’s even more important if you work with other people on the same files, on different versions of the same sources, with people in different locations and with different systems. The problem I currently try to solve (or, at least, try to bring a solution to) is the following … The system doesn’t initially use any revision control software. People are able to edit any file they want, one at a time (file locking which is very annoying). Basically, there is only one version of a file per project: the current one. If another project tries to merge the same file from another project, someone has to manually review all the lines in order to see what should remain and what should be left. In order to reach a previous version of a file, you have to manually remove lines marked with the patch reference at a specific location on some lines (it does work in some programming languages and not at all in all others). In fact, a rudimentary revision control system exists but it’s completely outside the development environment. When a file is modified, it’s name is entered in a “patch system” with the reason why it was modified (when you are lucky). If you forget to enter its name, the system can’t do anything for you (since it’s not aware of anything). ...
IPGphor2reader is a software meant to parse log (text) files resulting from an experiment with the IPGPhor and to plot graphs. I previously hosted it on my personal website and just moved it to Sourceforge, here. Amongst the various reasons for this move, I wanted the possibility for anyone to participate in the project and no hassle to manage this. Slowly, slowly, most software on my website will be hosted on Sourceforge or Bioinformatics.net. ...
BioMed Central is one of the main Open Access publishers in the world of Science, Technology and Medicine. On a side note, that’s where I published my two articles (in Proteome Science and the Journal of Circadian Rhythms). One might think that, given their support to Open Access, they would also support Open Source software and Open Format documents. For the software side, it’s not very clear. Although they ask authors to consider releasing software described in publications under a free (or at least open source) license, they also support and advertise for a bunch of proprietary software. While it’s not a bad thing per se (it enlarges the number of potential authors), it’s sad to see they don’t cite popular free software like OpenOffice.org (to write your article), Gimp (to edit your figures) or Zotero (for reference management). These are the three main software in each category but the free software world has many more of them! ...
Sometimes, even if you mainly develop on Unix/Linux boxes, you are stuck with MS-Windows on your desktop. Moreover, although your are a developer (i.e. someone who is supposed to know how to run a computer), you have no administrator rights so you can’t install the right tools that can improve your productivity and enhance your code stability/security. This is for the sad part. Fortunately, Free Software are there and most of them can even be run without being installed on your machine, just copy the software and use it! Here is a list of some of the software I’m using. Feel free to promote your favourite application in the comments. ...
Fosdem is “a two-day event organized by volunteers to promote the widespread use of Free and Open Source software”. I will be presenting Gemvid during a lightning talk on Saturday :-)
Finally, I got a working pixel lapse software under Linux :-) It’s a bit late (and I have to work tomorrow), code is rather dirty but I’ll publish it as soon as possible (btw that’s why I needed a webcam and a library to read it yesterday). Originally, “pixel lapse” photography is the process of creating an image one pixel at a time. Beginning in the upper left corner, pixels are captured sequentially at a set rate until the entire image is formed. ...