Posts By Giorgio
What I Think About When I Think About Manuscripts – I, Editor – Henry Gee’s blog on Nature Network
Perhaps what I am getting at is that scientific papers tend to be static. The best literature – of any kind – has a beginning, a middle and an end, in which the protagonists undertake some kind of journey, whether geographical or spiritual, and are changed by their experiences. In scientific papers, the results often give us no clue to the back story – the reason why the researchers were studying this system or that, and the tale of chances and mistakes and serendipity that led them to that point. The only readable parts tend to be the introduction, in which literature is summarized (a classic case of telling but not showing) and the discussion (in which the new result is integrated into what is already known).
via What I Think About When I Think About Manuscripts – I, Editor – Henry Gee’s blog on Nature Network.
GPG Key
I decided time had come to get a [[Pretty_Good_Privacy|PGP key]].
Here is my public ID:
1024D/DE8D92BF
This is my fingerprint:
6BA6 61B1 A198 8DDF 50BF 7F2A DE7F 773B DE8D 92BF
And from here you can download my public key.
Additional notes:
Quick notes for GPG syntax (here)
Creating SSH keys (here)
Project GREAT: General Relativity Einstein/Essen Anniversary Test
This is kind of old (goes back to 2005/7) but fascinating. This guy got 6 atomic clock. He left 3 at home and he took the other three to a weekend outing on Mt. Rainier (~1500 meters above) – along with his three kids, of course. All this to test one of most famous Einstein’s postulates. Here’s the link.. Don’t miss the family pictures section.
Videocapture for linux
If you did some hacking with a webcam and python, you probably ended up using the Videocapture module by Markus Gritsch. Unfortunately, the module does not work on any operative system other than windows, which could be a problem if you wish to make your application platform independent. So, here you will find a linux version of Videocapture. It has been tested on ubuntu distributions. It will run as long as you have installed
- python 2.5 (maybe others too)
- PIL – the python imaging library
- opencv
You can download it here. Some functions are actually not active (namely those that would call the configuration panels). It should work on mac too. Please, if you try it on a mac, let me know how it went.
Enjoy.
WinGooglizer
If you are a Linux user you probably already know and appreciate that (amazingly) simple piece of software that is googlizer. If you don’t know what I am talking about: googlizer is a tiny gnome applet that sits in your taskbar; everytime you click on it, it will start a google search using the text in your clipboard as query. Just select the text using your mouse to copy it in the clipboard, then click on the G icon of googlizer and voila, your google search is already waiting for you in your favorite browser.
Being myself a ubuntu user I love the googlizer but sometimes I need to work on computers running windows OSs. I decided to invest 20 minutes of my time (while waiting the confocal to do its work) to make a windows clone of Googlizer.
You can dowload it from here (it’s free, as in free beer of course). To completely emulate X copy&paste functions you may want to consider using True X-Mouse Gizmo as well.
Is written in Python then compiled to exe using py2exe and the installer is build using Inno Setup. In case you are interested in the source, here you’ll find the python code for wingooglizer, the py2exe setup file and the iss inno script.
WinGooglizer works fine on windows xp, sp3. I guess it will work on any Windows OS. Enjoy and let me know how it works for you.
pySolo: a complete suite for sleep analysis in Drosophila
Bioinformatics. 2009 Jun 1; 25: 1466-1467
pySolo: a complete suite for sleep analysis in Drosophila
Giorgio F. Gilestro, Chiara CirellipySolo is a multi-platform software for analysis of sleep and locomotor activity in Drosophila melanogaster. pySolo provides a user-friendly graphic interface and it has been developed with the specific aim of being accessible, portable, fast and easily expandable through an intuitive plug-in structure. Support for development of additional plug-ins is provided through a community website.
Availability: Software and documentation are located at http://www.pysolo.net. pySolo is a free software and the entire project is leased under the GNU General Public License.
Journal Filtered Pubmed
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| Cell | Nature | Science | |
| PLOS Biol | PLOS ONE | PNAS | |
| Neurobiology Journals | |||
| Neuron | Nature Neuroscience | J. of Neuroscience | |
| Nature reviews in Neuroscience | Trends in neurosciences | ||
| Development and C.B. Journals | |||
| Development | Genes and Development | Current Biology | |
| Nature Cell Biology | Developmental Cell | J Cell Biol. | |
| Embo Journal | J Biol Chem. | ||
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| PLoS Genet. | Nature Genetics | ||
| Immunology Journals | |||
| Immunity | Blood | Nature Immunology | |
| J. of Immunology | Immunology | ||
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Instruction From this page you can easily interrogate the PubMed database by restricting your queries to only certain journals. This feature is not available on the Pubmed site. Check the box next to the group category to include all the journals belonging to that category or select the journals one by one. |
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Widespread Changes in Synaptic Markers as a Function of Sleep and Wakefulness in Drosophila
Science. 2009 Apr 3;324(5923):109-12
Widespread Changes in Synaptic Markers as a Function of Sleep and Wakefulness in Drosophila
Gilestro GF, Tononi G, Cirelli CSleep is universal, strictly regulated, and necessary for cognition. Why this is so remains a mystery, though recent work suggests a link between sleep, memory, and plasticity. However, little is known about how wakefulness and sleep affect synapses. Using Western blots and confocal microscopy in Drosophila, we found that protein levels of key components of central synapses were high after waking and low after sleep. These changes were related to behavioral state rather than time of day and occurred in all major areas of the Drosophila brain. The decrease of synaptic markers during sleep was progressive and sleep was necessary for their decline. Thus, sleep may be involved in maintaining synaptic homeostasis altered by waking activities.
Redundant mechanisms for regulation of midline crossing in Drosophila
PLoS ONE. 2008;3(11):e3798. Epub 2008 Nov 24.
Redundant mechanisms for regulation of midline crossing in Drosophila.
Gilestro GF.During development, all neurons have to decide on whether to cross the longitudinal midline to project on the contralateral side of the body. In vertebrates and invertebrates regulation of crossing is achieved by interfering with Robo signalling either through sorting and degradation of the receptor, in flies, or through silencing of its repulsive activity, in vertebrates. Here I show that in Drosophila a second mechanism of regulation exists that is independent of sorting. Using in vitro and in vivo assays, I mapped the region of Robo that is sufficient and required for its interaction with Comm, its sorting receptor. By modifying that region, I generated new forms of Robo that are insensitive to Comm sorting in vitro and in vivo, yet still able to normally translate repulsive activity in vivo. Using gene targeting by homologous recombination I created new conditional alleles of robo that are sorting defective (robo(SD)). Surprisingly, expression of these modified proteins results in phenotypically normal flies, unveiling a sorting independent mechanism of regulation.
Regulation of commissural axon pathfinding by slit and its Robo receptors
Annu Rev Cell Dev Biol. 2006;22:651-75.
Regulation of commissural axon pathfinding by slit and its Robo receptors.
Barry J. Dickson, Giorgio F. GilestroCommissural axons grow along complex pathways toward, across, and beyond the midline of the central nervous system. Taking commissural axons in the vertebrate spinal cord and the Drosophila ventral nerve cord as examples, we examine how commissural axon pathfinding is regulated by the Slit family of guidance cues and their Robo family receptors. We extract several principles that seem likely to apply to other axons and other contexts, such as the reiterative use of the same guidance molecules in distinct pathfinding decisions, the transcriptional specification of a pathway, the posttranscriptional regulation of growth along the pathway, and the possible role of feedback mechanisms to ensure the fidelity of pathfinding choices. Such mechanisms may help explain how a relatively small number of guidance molecules can generate complex and stereotyped wiring patterns. We also highlight the many gaps in our understanding of commissural axon pathfinding and question some widely accepted views. We hope that this review encourages further efforts to tackle these questions, in the expectation that this system will continue to reveal the general principles of axon pathfinding.