MonthJune 2011

How to get your thesis in

A friend of mine, Julia, has written a little guide to classic things required when writing the thesis and the setting up for the viva, which apply for EBI predocs enrolled with the University of Cambridge.

This was a piece on our internal wiki (which nobody ever reads because is a closed one and it’s rather impossible to find, but the problems with closed wikis is a topic for another post). So I asked her if it was ok to grab it and post it here, which, at least, is in the open of the internet sea, and people could maybe actually find it with google or any other way.

These information were correct up-to June 28, 2011. As the matter of fact, she is now a Doctor :). Bare in mind this applied for a PhD thesis in the Biological Science umbrella, and the last part is EBI specific. Therefore is not at all official, they are just tips and hooks to speed up the process. Check always the latest rules from the University.

With that said, here you have it.

P.S.: Template-wise check out the amazing classic thesis. You’ve got to tune it, just a bit.

Thesis submission and viva

Written by Julia Fischer on June 28, 2011

When the time has come and you would like to submit your thesis to the Board of Graduate Studies, there are one or two things you might want to know.

1. Find a template

Most people (at least in the natural sciences) will write their thesis in LaTeX. There are a various templates out there. Please add your template here if you have found a nice one.

2. Restrictions and rules for the thesis

If you are submitting to the department of Biology, you will have a word limit of 60,000 words, but you can always check the newest information here.

3. Abstract and examiners

It is a good idea to start thinking about your examiners a couple of months before you submit. You will have to email the degree committee (, saying that you will submit soon. They will then send you a form to fill. You have to submit this form with your thesis title and planned submission date back to them together with your thesis abstract (which shouldn’t change significantly from there on).

They will then contact your supervisor who has to suggest two examiners for your viva. You might want to mention this to your supervisor in a meeting before you have to submit the forms, so you can discuss possible choices. One examiner needs to be internal (i.e. University of Cambridge) and one external.

4. Initial submission

When you are ready to submit, you need two soft-bound copies of your thesis. If you are sure that there will be no corrections, you can submit a hard-bound copy directly, but if you need corrections, you will have to pay for the expensive hard-binding again. Here is a lot of information about all the forms and declarations you need on submission day.

5. Your viva

It is advisable to try and set your viva date for the end of the month if you are going for the bridging postdoc contract, because you will receive the postdoc stipend from the 1st of the month *after* your viva. That is, if your viva is on the 1st of the month you will lose the pay raise for a full month.

Poke your supervisor to email the graduate office in Heidelberg and HR at EBI directly after your viva to confirm that you have passed and theat he/she would like to employ you as a (bridging) postdoc, so they can prepare your postdoc contract.

Good luck!

6. Submission of corrections and hard-bound copies

You do need to submit a hard-bound copy to the Cambridge University Library, although you may have to hand the copy to the degree committee, if you are faster that Cambridge burocracy. EBI will usually pay for the hard-bound copy that they would like for their own library, but you will probably have to pay for the other copies yourself. All about submitting hard-bound copies can be found here.

7. Congratulations!

You’re done!

+1 per l’idea di Civati

plus one

credits Macca su Flickr.

Credo che scegliere i candidati con le primarie, per rendere il porcellum completamente inefficace e ridare la possibilità ai cittadini di scegliere i candidati sia un’idea necessaria ed estremamente intelligente.

Questo avrebbe almeno quattro conseguenze:

  1. attiva partecipazione per le candidature, specialmente da parte di forze nuove (candidati) che avrebbero la possibilità almeno di farsi conoscere ed avere una chance
  2. partecipazione allargata a tutti quelli che vogliono dare una mano, con conseguente allargamento del partito e di ownership dello stesso. È noto che se una cosa la senti tua, ci tieni di più
  3. ridemocratizzazione delle scelte, con completa distruzione dell’effetto antidemocratico del porcellum, che vede il parlamento pieno di nominati, invece che di eletti
  4. dimostrare con dei fatti simbolici, che no, ‘destra sinistra, non sono tutti uguali’

E’ un pò allucinante che solo Civati sia quello che sostenga questa idea. Io, nel mio super piccolo, una +1 lo metto.

Numpy, Scipy and friends

I’ve just added a CC BY-NC-SA 3.0 license to my (one year old) presentation about scipy and numpy and imported the code and the stuff on github, so it’s easier for people to download it (and hopefully the link will not go down, after I’ll leave the EBI)

I’ll put it also here, so you can have a look.

Backup made it easy



Having a Dell XPS M1330 is kind of a problem. This computer failed me 3 times in the last 3 years. The mother board managed to cook itself every time, and also the graphic card died. It seems the problem was due to a lazy fan, which was not spinning as it should have done.

In this situation, coming up with a backup schema is necessary. More over a hot-backup schema, which permits to swap computers, going from the dead laptop to another working machine on the fly would be very convenient.  The other machine would be either my desktop computer at work, or my old (2003) acer laptop.

Usually I work with three different type of formats: code, simulations result and written report (in the form of text documents or presentations).

My simulations’ results live on the server @EBI, so I don’t have to care about the backup and I can mount/access them using ssh.

This leaves out the code and the documents.


For the code my choice has been to use git and host the code somewhere. For example Neuronvisio lives on the github repo. For stuff that can’t go live (yet) I’ve set up my own private git repo on another server, and I wrote a quick how-to here.

Given the distributed nature of git, to keep all my machine in synch, I just need to clone the repo. Then I can develop on my working machine (no pun intended) and I can push the latest development back to the online repo. When I switch machine, I just need to pull the repo to go up to speed. Easy and slick.


I think one of the best way I found to keep my docs synced is with DropBox.

Dropbox syncs automatically your docs (or any stuff you’ve got in the folder) with an online server. So you have an easy way to do the backup. What is more interesting is Dropbox allow you to add another computer to the same account, and automatically syncs the documents between the online computers.

Basically it acts as a bridge between your two computers, without having the problem to think about the backup, but automatically doing that. It integrates in a really nice way with Linux as well.

So join it and give it a go!

P.S.: If you use this link to join DropBox, I’ll get some free space 🙂


Using git and dropbox I have a complete automated backup system, which lets me to:

  • backup my code and docs with no effort
  • switch between different machines in no time, without worrying of data loss due to hardisk failures.

Comments are open if you want to share some other solutions 🙂

Stuff that I was saying for the last 14 years

Berlusconi Screwed Italy Economist


Also the Economist arrived to the same conclusion.

P.S.: In Italy this is well known, at least for a minority of the population.

Il fotovoltaico costa meno del nucleare

fotovoltaico-nucleareQuesti sono impianti di utility di almeno un MW di potenza. Il KWh fotovoltaico costa meno del KWh nucleare. È da sottolineare che le assunzioni e le premesse fatte dall’articolo non sono per niente tenere con il fotovoltaico, anzi chudono un occhio sui vari costi aggiuntivi ma mai presi in esame del nucleare (tipo chi è capace di fare l’arricchimento dell’Uranio, i costi dello smantellamento della centrale a fine vita, le scorie….)

L’articolo completo lo trovate qui.

via NTE.

360 degrees of sutainability

Sustainability will be one of our necessary new behaviour that we will need to endorse. Rethinking the way you leaving, making a way to get your life more harmonic with the planet, reducing the carbon footprint, growing your own. These can be some of the actions that could be taken to change a bit.

Jade has a very interesting post about sustainable heritage, going through in details about these aspects and not only. Check it out.

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