An Eye to the World, an Eye to the Net
<
p style=”text-align:left;”>Bioinformatics zen has delivered the result of some first analysis on the poll that we have spoken before.
It seems we have a quite pretty happy community 🙂
<
p style=”text-align:center;”>
Analysis from Michael Barton
The analysis are available from OpenWetWare
Have a look over there, or download the data and make your own!
So if you are using tiddlywiki you know everything, if you don’t you maybe want to take a look to it.
What is tiddlywiki good for?
For me is good as an advanced lab book. Yes an electronic labbook. All my biology friends have a really good fashion old school labbook, but I’m not too much into paper and I keep forgetting things.
More over is really a pain to search on the paper… I have different thoughts and ideas that are completely disconnected and only at the end they make sense (sometimes…)
So here the User Case:
If you recognize this, you want to give a try.
Now I want to suggest you two plugins (I started to write this post because the second one was really hard to find again, so I will put the right link here. I don’t think google is going to care too much about this blog, but anyway it could help a bit)
First of the latex plugin (if you don’t know what is LaTeX … well I’m sorry..)
The second one is the listTaggedTiddlers
Give it a go.. It’s really cool.
The bioinformatics survey proposed by Bioformatics zen during july is over.
As expected the USA is the country with the numerous entries, but France in second place looks to me as a surprise.
As usual Italy is one of the last country for number of entries (but at least is there :))
Into macro regions the Europe is rocking!
Have a look the other initial charts here.
More to come.
I have a constant itchy that I cannot get rid off: I want a smart and cool LaTeX editor for GNOME.
I would like to have something light and with a bunch of functions that could make my life easier.
Right now I use winefish which is doing a great job.
Strengths of this software:
One big problem:
It seems the way to go is enchant.
Now, winefish is written in C and it’s not really my cup of tea…
What I saw is that there is this pyenchant and the interesting bit is here
It seems there is going to be a support for the LaTeX filter soon (hopefully). This means that if there is an editor that is able to implement the pyenchant API we (if you read ’till here is also your problem…) have resolved our problem about an editor with a correct spell checking in LaTeX mode.
So looking around I stumbled to this scribes.
It seems to be under big development (infinite development?) but it seems the version 0.4 will implement the pyenchant.
Now I see two possible solutions here:
So you’re thinking that I should go for scribes. I don’t htink so, the autosave function will kill me and there is no undo function.
So maybe you said that I should look to GEDIT again and think about the LaTeX plugin… ‘Cause GEDIT will use or is going to use enchant. I’ve tried. I didn’t like it. I use GEDIT to open every txt file whatever is the content. So it should be light and quick. I said light and quick. The plugin is getting my GEDIT really slow. MKore over the spellchecker it’s not working.. So what we are talking about?
I would like to fix my first love winefish.
Or maybe stick to reality. Use winefish and run
aspell -t -c file_to_check.tex
or even use Texmaker
The spellchecker works really well, but I’m missing my powerfull shortkeys that I have in winefish.
Or maybe I should write another bloody editor in the right way (TM). (I won’t to reinvent the wheel for the n+1 time. It’s stupid and it’s not the way to do it.)
Suggestions?
I just discovered that all the translations in launchpad have to be under BSD license. Here is the FAQ
You have until the 31st of July to agree. If you don’t the only option is opt-off. (Yes, they are going to be removed…)
So it seems that Bioinformatic Zen has launched another interesting idea:
Why we don’t get the data about all the bioinformaticians around ad see what they are doing, to have at least a snapshot of what’s going on in the bioinformatics field?
So, to do that, a survey has been developed. The data gathering has started the 1st of July and it will be on up to the 1st of August. The data will be analyzed by all the people that want to do it and the result are going to be made available on the (proposed date) 1st of September.
For your convenience also YANNB will post the result.
Fill it if you have 5 mins :).
When latest GNOME went out with the marvelous clock-applet there was not too much hype about that. I think it was wrong. Check out the screen shoot 🙂
Isn’t that cool?
If you wondering what is the other stuff … well one is the failed tentative to run nest through ipython , the other is eclipse with a quick and dirty java program…
Arata Phenomena: this is the name given by the scientists to the reaction of cold fusion obtained by Arata in Japan just few hours ago.
The deuterium (isotope of the hydrogen with one neutron) was pumped into a reactor where there was a cathode formed by 35% of palladium, and 65% of zirconium.
The reaction started to produce energy activating a thermic engine. After one hour and half the experiment was stopped to measure the amount of Helium-4 produced, sign of the reaction.
That’s a really good news
Sole24 Ore (italian site)
More info here
Scientific publication here. More info also here
via Beppe Caravita
Tomorrow, 22th of May, in Osaka, Japan, the professor Yoshiaki Arata will try to demonstrate with the first public experiment on a big scale that the cold fusion is possible and it works.
I hope it will work. It will change a lot of things…. More on this later on…
Update: The experiment worked! More here
Modeling in biology is a kind of Cinderella branch of the field. Is not central as it is in physics and there is a lot of skepticism about it, especially from the wet lab guys. Biology has started as a descriptive subject and then it went to the quantitative approach.
Quantity. That’s exactly what you need if you want to do some modeling, that at the end of the day is crunching some numbers using a computer.
Let me just make a comparison with the engineering field. This guys usually:
If for example you’re building an house, you hit a button and the program is going to make all the calculation to see if the house is safe and it will last, or it will just collapse under its own weight. Actually you’re testing your idea, modeling it on a virtual space.
In biology you have the same kind of approach:
The modeling should be one point of the design part to let you know if your experiment would discover something or not, so you can save time and know on which parameter focus your attention or which proteins seem to be the important key role. It should help the biologist to design better experiment.
For example you have a cascade signaling involving something like 15 proteins. If you have a tool that is going to predict that the most interesting reaction over there involve protein 2 and protein 3 you can focus your attention over there, avoiding the scan of all the other proteins in the first place.
To do that we need of course a really rock-solid modeling framework and from the other hand a really easy and fast way to use it.
We are quite far from there, but it looks to me like an intriguing prospective.