SYBIR: Synthetic Biology Ideas Reactor

Everything started with this tweet of mine:

I often have ideas about synthetic biology project and I'd like to discuss them with other people, getting feedback, improving the idea and why not find someone who could realize that.
Using Ubuntu I'm familiar with Ubuntu Brainstorm (click on the link to understand what is it and how it works) and I thought that it is a clever and very democratic system to talk about ideas and to improve something (in this case the Ubuntu OS).

It's based on IdeaTorrent:

an "open innovation software": it lets people submit their ideas, brainstorm them, and vote on them. The most popular ideas and requests are then easily assessable.

So I involved in my project on porting IdeaTorrent to Synthetic Biology my friend Gerd Moe-Behrens from Leukippos Institute (follow him on Twitter, he is very active user with a lot of tweet about synbio: @Socrates_Logos). He is very enthusiastic about the project indeed he started a conversation on his website to outline the main features that the project shoud have and I warmly recommend you to join it and to share your thoughts and ideas.

How will it be different from IdeaTorrent?
Our customizations will be these:

• every user (researcher, lab, interested person) has a unique id which can be used on publication as a reference to the SYBIR site
• there will be the chance for lab to sign up; the user signed as Lab will be able to choose to develop a specific idea, doing experiments and writing papers on it and everything will be public on the page of idea itself making the feedback from other users an important part of the process

This is still a work in progress therefore if you have any other ideas, suggestions or you want to be an active part of this project you have just to write on the page of the Leukippos Institute.

The big issue with this project is the license an idea should have and how every part contributing to the idea should be rewarded (more on the page of Leukippos Institute).

I hope you could join us and making this happening either better and faster.

SYBIR (SYnBio Ideas Reactor):
Easy to use idea submitter for people with an interest in synthetic biology

Join us here: http://www.leukippos.org/Leukippos_Institute/Blog/Entries/2011/5/17_IdeaTorrent.html

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[Idea at proof stage] Using Facebook for Correlational Research

First of all I have to admit that I'm a very newbie in statistical science (let's say I know one or two things) and that all of the ideas wrote here are just speculation coming from my mind.

I'm quite obsessed in finding patterns in things.
I noticed that people looking alike have some similar behavior, same physical features.
In genetics with the term linkage we indicate the tendency of certain alleles to be inherited together because they are physically close to one another of because it's important for some reason that they don't assort independently.
Linkage is often used to discover genes related to diseases.
In my opinion we can extend its definition and use it not only for the purpose I've just mentioned above but it could be useful also for discovering protective factors for diseases.

My idea is to see correlation between people's medical history and their:

• habits
• sexual life
• work
• sex
• age
• family history
• social condition

and for this purpose I want to use the largest database in the world of human beings: Facebook.

Since some months I have been thinking about how many data we put into social networks spontaneously and how this data, with relation to our connections (friends, parents and relatives), could form pattern that not a human being but a computer can understand and extrapolate (it's called Data Mining and I just discovered this today).

I still don't know how to sort this out, by now I plan to develop a survey Facebook application.
But with this approach there are some problems:

1. Noise: people can answer questions with false information
2. Appealing: people wouldn't reply questions for no reason. I have to make the application appealing and develop a game around it (e.g. Find your partner, Who looks like you, ecc...) 
3. Harshness: Facebook it's just for fun and of course I can't ask: are you obese? are you rich? Questions have to be asked smoothly and indirectly: Do you like eating? What mobile phone have you got?

The application would also continuously monitor some information from users:

• from status update it can get information about an user habits, what he eats, sports he practices (why not, even sexual habits)
• from new options of geolocalization it can check places he attends (e.g. where he spends much of his time that can be a gym or a McDonalds)
• it can even understand if he spends too much time on facebook from pc (so he has a sedentary life-style) checking how long is he online (and assessing he is active of course)

Everything about this idea is still a jumble in my mind and I hope to sort this out soon and whoever wants to be involved has just to comment this post.

Follow me on twitter for updates

By now I have the support from Moreno Colaiacovo (@emmecola) from MyGenomix who gave me some useful advices and I hope more people will join this project.

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Random Ammino Acids Abbreviations Generator

I have to learn amino acids abbreviations for my Proteomic exams.
Therefore I created a very simple script that gives me, every time I start it, the amino acid abbreviation.
So, when I read it, I can write its structure on my paper.
This is the bookmarklet: AA abbreviation generator.

If you want to make it 'interactive' to have a feedback if you guessed right, I made this other bookmarklet: AA Abbreviation name Quiz.

Bouns: pK_i(-COOH) quiz

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[How To] Watch Filmon.com streaming on Linux

Maybe you already know this http://www.filmon.com
Until it will last, it broadcasts some international tv channels (BBC, CNN, CBS...and porn as well).
It works "software-less" on iPad, iPhone and Android.
On Windows it need a software (downloadable from the site itself) and on Linux you can run it with Wine with no problems.
But I didn't want to use it because it requires too CPU work therefore I thought about a workaround (works only on Firefox since on Chrome you can't change your user agent) and the principle on which it is based is to emulate the browser of Google Nexus One.


Follow these steps:

1. Install the extension User Agent Switcher and reload Firefox 
2. From Tools Menu search for something like "Default User Agent"
3. Click on "Edit User Agent"
4. Click on "New", then on "New User Agent..."
5. In "Description" field write whatever you want (e.g. Google Nexus One)
6. In "User Agent" paste this string: "Mozilla/5.0 (Linux; U; Android 2.1; en-us; Nexus One Build/ERD62) AppleWebKit/530.17 (KHTML, like Gecko) Version/4.0 Mobile Safari/530.17" (without quotes of course)
7. Empty other fields and click Ok
8. Now go on http://www.filmon.com and choose the channel you want to see
9. Choose Totem or VLC as software to reproduce the stream
10. Enjoy!

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Medioman

Non mi scandalizzo di quello che ha detto B oggi, cosa c'è di nuovo/strano?
La cosa triste, e vi invito a contraddirmi, è che se vi guardate intorno, dal tabaccaio all'autista del bus, quanti non la pensano esattamente allo stesso modo?

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Cos'è un PhD?

PhD sta per Philosophiæ Doctor e può essere tradotto con il termine italiano di Dottore di Ricerca.
Per capire bene cosa significhi ho pensato di tradurre in italiano un'affascinante quanto semplice e diretta presentazione fatta dal Prof. Matt Might, docente di Computer Science presso l'Università dello Utah.
Segue la traduzione  dall'originale (The Illustrated Guide to a Ph.D.)

Ogni autunno, spiego ad un nuovo gruppo di studenti dottorandi cosa il dottorato sia.

È difficile descriverlo a parole.

Perciò, io uso le immagini.

Leggi sotto la guida illustrata al dottorato di ricerca.

Immagina un cerchio che contenga tutta la conoscenza umana:

Nel momento in cui finisci la scuola elementare, tu ne conosci un po':

Quando finisci la scuola superiore, ne sai un po' di più:

Con una Laurea Triennale acquisisci una specialità:

Una Laurea Specialistica approfondisce questa specialità:

Leggere pubblicazioni scientifiche ti porta al bordo della conoscenza umana:

Una volta arrivato al limite, metti a fuoco:

Spingi al limite per alcuni anni:

Finché un giorno il confine cede:

E, quell'ammaccatura che avete prodotto si chiama dottorato di ricerca (PhD):

Naturalmente, il mondo vi sembrerà diverso ora:

Perciò, non dimenticate l'immagine più grande:

Continuate a spingere.

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DNA Reverse Complement with Ubiquity for Firefox

Due to my lazyness and headcache staring at the monitor to create a reverse complement of a DNA strand, I create a simple Ubiquity command which does it for you.
It is easy to use:

• select the DNA strand in plain text format (I preferably use this command for Primer3)
• activate Ubiquity (usually CTRL + Space)
• write the command revcomp
• you will see the reverse-complement counterpart of the DNA sequence you selected
• to copy it just press enter and it will be copied in your clipboard

It is also possible to use it without selecting a sequence but writing it directly into Ubiquity.

To see the help, just write in Ubiquity: help revcomp

Install it: click here.

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