maltese

Computing…

 technology, university  No Responses »
Mar 232012
 

After 30 hours of computation the Big machine (30k € worth) spitted a .gz file of only ~440MegaBytes. I was suspicious about this size. It’s ok that .gz format compresses a lot, but this is too much. So I unzipped the file and after that I wrote a few lines of code to inspect this big file (1.5GigaBytes after decompression).
End… after 50 millions lines I noticed the file was incomplete!
Today I’ve runned another instance of the program, with a lot of improvements. Memory usage dropped! Not so drastically, but it is still a good news. Even time is employed much better. Only 30 seconds per compound instance! In this way my matrix will be ready by this night.

Toshiba issues and some music

 music, technology  No Responses »
Mar 172012
 

Today it’s been a bad day. I argued at the phone for hours with the Toshiba call center. I’m experiencing issues with my laptop but the tech support did not noticed the problem. In the end they asked me to restore initial settings on the device. So I’m spending my friday night trying to get it back to initial status. Really boring. Thanks god I have my music!
Here’s a piece I’m listening a lot during these days!

iPhone firmware update

 apple, technology  No Responses »
Mar 132012
 

I did it. I was so afraid to make this move, but now I’ve done it, and I do not regret.
It was a very long time since I did not update my iPhone firmware. I was stuck to 4.3.3 for months. (Maybe it was june 2011).
In the wake of yesterday’s updates I found the courage to push the button and to update it.
First of all I was afraid of losing my data, so I made a backup of my photo gallery. Just to be sure I backed up everything on iTunes. And then… a dive in the dark. I’ve always had problems with updating, I’m pretty sure that it happened because I was using iTunes on my Windows PC. This time I’m using a MacBookPro 13.3″ and the syncronization and the updating worked both, as a charme.
Now I’ve my iPhone up to date and I’ve also been able to recover all sensitive data. Even applications have kept their settings and I’m so happy about this.
After few weeks of work with Apple products I feel quite free to say that they simplify user’s life a lot, it means that people feel much better to use software than to waste time setting it.

Updating followers

 university  1 Response »
Mar 132012
 

It’s been a long time since I posted here the last time. Not so much but I feel like I have to say something to keep my followers up to date with my work.
I’ve just finished a section of my thesis work. It is a part that can be exploded in several little parts (yeah, just like that principle.. divide et impera).
First of all I have to parse a tab-separated-values file that contains a certain amount of chemical compounds used on a particular cancerous cell line (MCF7). In this part the software goal is to search for duplicates in this list and to extract a subset of unique compounds. After that I query PubChem database to identify the little molecules and to retrieve additional information such as synonyms and SMILES formula. Then I operate a conversion on the SMILES formula to get a bitset format named fingerprint. Using Tanimoto/Jaccard similarity score I calculate the chemical structure similarity among the compounds. This last step generates a triangular matrix which I will use, along with other bio-genetic informations, to identify groups of pharmaceuticals that have the same effect and share some structural parts. But this is the next step.
During my work I had the opportunity to learn to use LaTeX, a great typesetting system. It is not so intuitive in the beginning, expecially if you’ve always been using word processors like MS Word or Keynote, but if you give it a try it will surprise you. It’s a very powerful way to produce scientific documentation. I’m using TeXShop and it’s pretty simple to learn to use.
Now I have to go to sleep because tomorrow starts the new section of the thesis and I want to be in a good shape! Goodnight!

Day 30 – my favorite song exactly one year ago

 music  No Responses »
Feb 232012
 

Thanks god Internet exists! I have a very bad memory, so if I had to remember a song that I was listening to a year ago I probably would have failed.
My blog has date tags on each post, so I just got back in time and picked up a song that I’ve posted on feb 17th.
But I don’t want to re-post it, so I’m going to suggest another one by the same artist and that I was surely listening to one year ago. Enjoy!

 Older Entries  Newer Entries