Category: English

The last ride

July 8, 2011 / / 0 Comments

atlantis take off

The shuttle Atlantis is in the space. Today for the first and last time, I just followed the launch in streaming from the NASA tv. Before I saw only movies with the shuttles, like the sci-fi Armageddon.

But today I was able to follow the whole launch, just streamed directly from the NASAHDTV channel.
I’ve followed the lift-off’s procedures and I saw it live. It was emotional.

Thinking that after 1 min and 40 seconds the Atlantis was already up in space. It was possible to see our planet just down below. These guys were up in space. And yes I know there is the ISS floating up there (BTW it’s exactly where the shuttle is going) with people inside all the time, but seeing the stream and thinking that in so small amount of time the shuttle was flying so high it’s something big.

Now the shuttle program will be shut down and NASA is looking for something new. Let’s see what they come up with, if funding holds. ESA and other players are still up and running, and also the NASA has some plans for the future.

For the time being, Soyuz spacecraft will be used to continue servicing the ISS.

The shuttle will be up there for another 10-12 days, will dock to the ISS and then come back home. Best of luck!

Anyway, I’m kind of sad. The shuttle was cool.

Last lift off, Enjoy the last ride.

How to get your thesis in

June 28, 2011 / / 0 Comments

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 (degbiol@mole.bio.cam.ac.uk), 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!

Backup made it easy

June 13, 2011 / / 1 Comment
backup

credits: http://askbobrankin.com/automatic_backups.html

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.

Code

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.

Docs

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 🙂

Conclusions

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 🙂

360 degrees of sutainability

June 6, 2011 / / 0 Comments

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.

Cappotto

May 31, 2011 / / 0 Comments

il vento cambia

Yesterday the run-off of local elections has been concluded. The LeftWing managed to win Everywhere. Yes exactly Everywhere, even somewhere it was seen as impossible, it simply won, beating Berlusconi’s party and the xenophobic Lega Nord.

Think about a card game, where the other guy does not score at all, and you’re able to make all the points. Well, we call that “Cappotto” in Italian and pretty much is what happened yesterday in Italy.

The leftwing won Milan, something that was not happening from a lot of years, the main city and headquarter of Berlusconi, with a compact leftwing, made by three different parties. The rightwing has been beaten also in Naples, where the candidates has been adopted in the run-off also from the leftwing, coming from a party which was in coalition in Milan, but not in Naples. (too long to explain here.)

Turin and Bologna has been won on the first round.

Another two big cities are Triest and Cagliari, which usually has always been on the rightwing have won by the leftwing. The sweet spot is also Arcore, Berlusconi’s hometown, has been won by the Democratic Party and the leftwing, with a woman as candidate for major.

A new vibrant energy was flowing yesterday, and today everybody has re-gained the hopes that a change is possible.

We won, and in amazing good way, among all the Nation, from the small to the big cities, from South to North, from East to West in the 150th anniversary of the unification. Today is a good day. As inspired by the end of Pisapia’s campaign in Milan, let me say

Buongiorno, Italia.

Dear Europe

May 13, 2011 / / 0 Comments

Please don’t do it.

Please, let’s not go back 30 years. The freedom to circulate in Europe as an European citizen is one of the most important freedom that has made our life easy.

Moving around, using the Identity Card, or the Passport, without having the necessity to apply for a visa or anything like that makes not only everything super easy and nice, but also gives a feel to be all the same, within the diversity. Together with the Euro and the flag these are the only tangible signs of an integration which has gone far, but has not yet complete..

We have to go to a more integrated system, where all Europe should be felt as our home. With the diversity of culture, language and maybe attitude, but still one big jam of people who leverage the strengths of each other and try to solve the weakness. The European Community, not only a political body, but a community of different people.

I understand this terrible wave of extreme right, with its xenophobic and racist ideas, is taking its toll on the possible decisions. But I think the other parties should make a stand. They should fight back this narrow-mind vision.

European Flag

Europe has been born by the vision of people who are now long-dead (Jean Monnet, Robert Schuman, Paul Henri Spaak, and Alcide De Gasperi), and who built this ensemble as a way to achieve peace and better conditions for everybody.

Europe should be at the forefront of integration, leading with a peaceful and calm approach, as an old continent should do. We’ve got tons of history and we did a disaster in the last century.

Let’s take another seat on this one.

Let’s make this one worth remembering as the century in which Europe took the lead in making the world a better place, starting within its own frontiers.

Let’s not think in three weeks span. Let’s think in 30-40 years time or even more. Let’s go ahead and make the European Community more connected and let it thrive.

In varietate concordia, United in diversity, Uniti nella diversitá, (Motto of the European Union), this is what Europe is.

This is why, this a great Community. And please, leave the door open, ’cause no Community is an Island. Let’s think BIG.

Unity and accents

May 1, 2011 / / 1 Comment

With the release of Unity and the (following) upgrade, I found myself with a problem that I thought to have solved long time ago: how to write accents. It turns out that the use of the compose key (Super/Meta … the one with the Windows logo) is used for the default shortcuts, which you need badly, to have a decent experience with unity..

The good thing is that I’ve discovered the layout UK – with WinKey which provides all the most classic accent like á é ó which can actually do the trick.

On another note I think Unity is pretty a good idea… But I have to use it a bit more to tell the true story..

Update: Actually I found out that on the UK -with WinKey the standard è is of the less used type (there are two: e acute (é) and e grave (è).

Now the last one is very important because is the third (singular) person of the verb to be (Today is a good day, Oggi è una bella giornata), therefore is used a lot.
I found a decent compromise using a US Layout with Italian letters:
Screenshot-Keyboard Layout "Italy US keyboard with Italian letters"

You get the accent with Alt-Gr.

HIH

Endangered species Symposium

April 20, 2011 / / 0 Comments

At the EBI there is an annual symposium which is organized by the Science and Society committee which I’ve been involved in the past years (some video are available on the youtube channel), but not this one. But no fear!

New people get on with the job and pull out a really nice symposium.

If you in Cambridge, you've got to come

This year the committee has chosen the topic of Biodiversity and Endangered Species, the 6th of May at Fitwilliam College Auditorium, Cambridge, Uk.

It’s free for all, so if you’re around don’t forget to come over 🙂

Yeah, there is even a Facebook event, if you are into that thing 🙂

Cesium contamination projections

April 18, 2011 / / 2 Comments

As you know there was a massive Earthquake (and there are still some going on) in Japan followed up by a massive nuclear accident at Fukushima I which has been evaluated 7 on the INES scale grade accident.

Now there are some prediction made by the University of Cologne about how the Cesium will spread around the world.

In the case it does rain

Cesium spreading Wet scenario

and it doesn’t look good.

And in the case it doesn’t rain

Cesium spreading Dry scenario

And it doesn’t look good at all.

Via Crisis