Category: Science

The Mortal Immortal live streamed!!

May 6, 2009 / / 0 Comments

If you are around Cambridge this friday and you are interested in science and society I would like to let you know that there is going to be a conference called:

The Mortal Immortal – Scientific and Social Aspects of Ageing

The good news is if you can’t make it you can see the event in live stream on ustream.tv on this link:
http://www.ustream.tv/channel/The-Mortal-Immortal—Scientific-and-Social-Aspect

At the final panel we are going to take questions also from the net, so don’t forget to join the chat and throw your question 🙂

The importance to have a VCS..

December 9, 2008 / / 3 Comments

…Or as Bazaar just saved me the day

In bioinformatics the Good Programming Practices are always seen as a “too big solution for a too small problem”.

BioinfoBlog is not of this advise and I totally agree.

For example the use of a Version Control System is always seen as an overdue for our project (classical objection: my project is just a bunch of scripts… yeah.. sure….).

Let me try to convince you with a real life example and why today bazaar save my day (or at least a lot of time).

Scenario: I was running a custom simulation of this model available from Biomodels database when I saw that something that before was working it wasn’t anymore!

The model encodes the really complex series of biochemical reactions that permits DARPP-32 (a protein present in the spine of the Medium Spiny Neuron) to integrate different stimuli (Glutamate and Dopamine releases) and to respond accordingly.

for the brave biologist or interested scientists between you I promise I will speak about this later on….

To better understand the model and simulate different input today (ok, the simulation started yesterday night..) I was running a simulation using a stochastic simulator. The expected result would be to have different output due to the stochastic variability but still quite similar.

Bear in mind that I will show you 4 copies of the same simulation that should diverge only for the stochastic effect; this means you should expect 4 curves that will be more or less of the same shape.

d_it_4

Doh!

In this image you can see the time courses of the molecules of DARPP-32 (D) in the not phosporilated state; there is a dramatic drop of this form of the protein because the input of Calcium activate several kinases that are going to phosphorilate DARPP-32. The input of Calcium is applied (technically is a train of Calcium) at 100s

The discrepancy between the four trajectories is too big and cannot be addressed to the stochastic variability only, but it looks like in three of the iterations there is the lack of the input (No Calcium applied at all).

So I took a look to the trajectory of Calcium to see if it was missing:

Calcium input 4 different iteration

Calcium input 4 different iteration

Eureka! The Calcium is not applied in the 3 of the four iterations.

If you thinking where is bazaar and why it saved my day… don’t worry! I’m getting there… It just takes time…

So I know:

  • which is the reason of the Bug
  • I know that I refactored the code some time ago to have the possibilities to ran different kind of simulations and I very likely introduced the BUG
  • I know the simulation was working before this point

I fired up olive and try to understand where and when I’ve changed this bit

Olive GTK screenshot

Olive GTK screenshot

The selected revision is the one where I refactored the code and added the new Experiment class to better shape my inputs, and the one where most likely I’ve introduced the BUG.

Rewieving the changes that I made I found out that I don’t create a new list of inputs for each iterations, but only for the first one, so when the other iterations check for the input to apply, they don’t find anything!

So I fixed the BUG, and I re-run the simulation and I’ve got the right results.

4 iterations DARPP-32 BUG fixed

4 iterations DARPP-32 BUG fixed

If I didn’t have bazaar installed or I didn’t use any VCS, I had to spend a lot of time to debug my code this morning with no clear idea where to look and what to change. More over there would be also the frustration to get something to work again when it was working before.

So if you are in bioinformatics or you like/have to program think about to use a VCS. I’m using bazaar because it’s easy, it’s distributed and it has also a really good svn-bridge-plugin, so I can push all my code to the svn of my group 😉

RessearchGate, the scientific facebook?

November 24, 2008 / / 2 Comments

The social networks is new direction of the web. Different kind of social networks create different kind of possible relationship. For example the network that I have on facebook has a small overlap with the network that I have in linkedin.

An email suggestion pointed me to a new kind of social network called researchgate.

Research gate logo

Research gate logo

for my usage this will hold the network that I have in linkedin, but as for all the social network, it has to grow to become a meaningful resource.

On the technical side I saw that it’s possible to import your library but right now the format accepted is only XML. I hope they are going to implement also the support for a BibTeX import, so I can test the semantic engine and take a look to the papers it’s proposing.

Anelando verità

September 30, 2008 / / 2 Comments

Su mentecritica c’è un bel dibattito su che cosa sia la verità.

Partito da un post di Cruman, continuato con un mio post e con l’ultima voce di zippole.

Innazitutto vorrei ringraziare zippole per la pseudo recensione del mio pezzo che qui riporto:

L’articolo di Mattions è Verità. E’ tremendamente vero. Un ragionamento, o meglio un discorso, che non faccia una piega, tenga i piedi incollati ai fatti, e allo stesso tempo sia così sentimentalmente sincero è vero per definizione. Sicuramente può venir “limitato” a Verità Soggettiva per il fatto di aver scelto un ambito di spiegazione piuttosto che un altro, ma in seno al discorso tutto è logico e nella mancanza di una soluzione lo stesso autore fa trasparire sinceramente il suo smarrimento.
Vorrei fare una mini analisi del testo, in particolare le ultime tre affermazioni:

* constatazione
* battuta per sciogliere la tensione e preparare positivamente all’ultimo punto
* riassunto dell’articolo per ribadire la mancata soluzione al quesito

E’ un po’ come il finale di un concerto con un accordo secco ad alto volume, una canzone che termina con un acuto piuttosto che con un calare. Essa non parla umane parole, eppure ci comunica chiaramente quello che vuole esprimere!
Questo articolo è corretto nella logica delle parole, ma è anche estremamente Vero nel messaggio veicolato dai toni!
Avete mai ricevuto una Vera consolazione, oppure siete stati contagiati da un entusiasmo, o provato un sincero amore sconfinato nella fase delle coccole?
Questa è relazione.

Devo dire che mi ha fatto realmente piacere e che ne sono estremamente contento.

Infine una frase veloce sul concetto di verità:

la Verità come idea platonica rimane nella caverna e la sua ombra che si protrae all’esterno ci confonde e ci illude. Tuttavia abbiamo bisogno di verità piccole e veloci, da utilizzare come metro di paragone per riuscire ad intenderci e raggiungere un accordo. E qui la scienza viene in aiuto per risolvere problemi contingenti.

La scienza può fornirci una verità contingente e ricamata sul soggetto in questione.

L’insieme di tutte queste piccole verità ci può aiutare a scegliere e capire quali scelte operare, sapendo che queste necessitano di una costante revisione.