“ The 'free' in free software refers to freedom: it means users have the freedom to run, modify and redistribute the software. Free software contributes to human knowledge, while non-free software does not. Universities should therefore encourage free software for the sake of advancing human knowledge, just as they should encourage scientists and scholars to publish their work.“

Sunday, June 20, 2010

GreenLab.py

See the link on the right of the page --->

GreenLab is a simple python code used to check the status of printed papers on a network printer.

I wrote this code to keep track of printed papers in my lab.
It generates a file (printer_log.txt) which store the number of printed page, the date and the time. It also converts the number of printed pages in percentage of dead tree (based on the information found in the Conservatree website)

If you want to use it you have to
1] Copy the text in your editor (I use Textwrangler)
2] add your printer's address (line#4)
3] Run the script in your terminal, check on the first temp_printer.txt file the line where the printer displays the number of printed pages and write that line index on line#8
3] save the file as GreenLab.py ... that's it!
whenever you open the file the script is run and it retrieves the information about printed pages (obviously you have to be on your local network to get those infos!)

Since it is made with python it 100% multiplatform.

I use it in combination with iCal on Mac.
(iCal periodically runs this script so I can have a log of the printed pages ... and I have the chance to control my tree-killing printer...)

Thursday, June 17, 2010

OSALT

Here you can "Find open source software alternatives to well-known commercial software"

BIG@EPFL

The Biomedical Imaging Group at the EPFL (Lausanne-Switzerland) has a website that is a gold-mine for image analysis.

Thay developed DeconvolutionLab, a plugin for imageJ implementing 2D and 3D deconvolution.

LOCI - Bioformats

The LOCI website has a cleaver plugin for imageJ to open raw files and import lots and lots of metadata.
Have look also at the other pages on bioformats for other softwares.

here is their mission:

"LOCI is a biophotonics instrumentation laboratory stemming from the research activities of Kevin Eliceiri, Dave Beebe, Bill Bement, Paul Campagnola, Patti Keely, Brenda Ogle, Justin Williams and other LOCI investigators. Our mission is to develop advanced optical and computational techniques for imaging and experimentally manipulating living specimens.

New and improved imaging instrumentation and optical-based experimental techniques are being developed. These projects are driven by demands arising from the scientific studies of external collaborators and the principal investigators and opportunities that arise with the emergence of new technology. Instrumentation development is undertaken in a form that is both accessible and beneficial to the scientific community.

LOCI is directed by Kevin Eliceiri, and all inquiries about LOCI collaborations or general imaging questions may be directed to him. "

Monday, June 14, 2010

Seashore



Seashore is a nice image editing software. Simple and clever!

LifeHacker

Lifehacker frequently posts free apps for both MAC and Windows.
The website is packed of useful (digital and not-digital) tips and tricks!

EnzimeX

New software added on the list:
EnzimeX - for people working on restriction enzymes.
(Thank you Yosuke!)

Sunday, June 13, 2010

VirtualBox

If you want to run software on different platforms (MAC-LINUX-WINDOWS):
VirtualBox

I tried Ubuntu 10.04 (Lucid Lynx), XP and WIN7 on a MacBook.

... useful when killer-applications (i.e. NeuronStudio) are not platform independent!

iPapers

Another Software for Academic reference management (iPapers - see list on the left) ! (Thanks Masa!)

If you are going to compare these two softws Mendely and iPapers ... let me know your preference!

Mendeley.com

Have a look at this Academic reference manager tool (Mendeley - see the list on the left)!
It looks great

Thanks Adam !

Saturday, June 12, 2010

Free - Open Source - Platform Independent

Scientific software should always be FREE, OPEN SOURCE, PLATFORM INDEPENDENT.