Mind the Byte has been selected to participate in the fourth edition of BioemprenedorXXI. BioemprenedorXXI is a program to support entrepreneurship in the field of life sciences and is powered by La Caixa, Barcelona Activa, Biocat, Genome Spain and the Chamber of Commerce of Barcelona.

After a preliminary selection, the twenty selected participants, including Mind the Byte, enjoy a few months of training to mature and to prepare the business idea. It covers various areas such as marketing, planning, legal forms and financing. Each participant is assigned a personal tutor and, in addition to training as such, attend conferences and networking lunches, investment forums and visit companies and research centers.

The award is very, very tempting, but the mere fact to participate in the program is already a prize.

Finally, I would like to congratulate the people of aScidea, who will be also participating in the competition.

A few weeks ago, in a conversation via Twitter, Álvaro Martínez told me about a project they were launching: “Notícies d’In”, a news portal of science and technology. Some days ago He contacted me to ask me for the inclusion of this blog to the “Planeta d’In” (a blog planet), a collection of blogs of science and technology, linked to the news portal.

Today presented two initiatives, Notícies d’In andPlaneta In.

From here, good luck and congratulations for the initiative!

I’ve wrote anything for several weeks. The reason is I’m working in a new project that requires almost all the available time and I don’t have enough time to post something. I hope I’ll be able to show something new in few hours or days.

Some months ago, the pharmaceutical research company, Palau Pharma, announced that the company will lay off 53 people. It is approximately the 63% of all company staff. All this people are good qualified people that works at different levels of the drug development, from technical staff to group leaders.

Yesterday I saw this people had created a webpage where they told this story and show a list of all affected people, with their role in the company. In addition, this page contains a link to the professional profile in LinkedIn for each of them.

In my opinion, a pharmaceutical company should be a company based on research, new drugs development, clinical trials and, finally, the commercialization of these drugs.

Pfizer is not doing it. I suppose (and I hope!) this company should has his scientific basis and his laboratories but a company which budget is based, basically, on the benefits derived from a product the has not been developed in his labs (Lipitor) and now, when the patent if going to expire next year, decides to buy new companies to obtain new products, is not a pharma company.

Lipitor is an anti-cholesterol drug. It was developed in 1985 by a company that was acquired by Pfizer. This drug is the most sold drug in the world and i the best product (in terms of money) of Pfizer. The problem for the company is that the patent that “protect” Lipitor (an Pfizer) will expire next year. It is curious that a company basis all of its budged in a product developed for a third company but, the worst thing is that this company has not been able to develop other products to compensate this patent expiration. Instead of do more research, Pfizer decided to buy companies to try to have new product.

I am agree that a pharma company is a business and can buy and/or sell other small companies. But it does not be the bases or the main business of this kind of company. A pharma company should invest most of its money in research. Sincerely, if Pfizer has not been able to develop a new product (or products) to compensate this patent expiration I don’t know if we are talking about a pharma company.

I understand that release a new drug to the market is really expensive, I understand that the clinical trials are more exigents,… But, if these small companies can do it, why Pfizer and other similar big pharma companies prefers to buy them instead of develop science by theirselves? Maybe because these small companies put almost all their budget in the research department instead of the marketing department.

Today is my first day at work after the summer holidays. Usually, when one start a new year (natural or academic) try to do new things. Today I am starting something new related with this blog: today I’ll start the English version of the blog!

On this blog I talk about science and about my job as a researcher. I started this blog in Catalan (my language) and I want to maintain it. But I also want to have more readers as possible and I decided to try to do a parallel version of the blog written in English.

Sorry if there are mistakes in the English version

Old posts of this blog are only in Catalan (my language). Translate all past post is too difficult and not affordable for me. In the future I’ll try to translate some of them but, actually, if you would like to read the old content of the blog, you can use online tools such as Google translate. Apologies for the inconvenience.

Moltes vegades tenim un conjunt de molècules i volem seleccionar, en un segon conjunt, aquelles parelles de molècules que més s’assemblen. Per exemple, tenim n molècules que hem vist que són actives per una determinada proteïna i volem buscar fàrmacs que s’hi assemblin (com més semblança, possiblement, millor semblança en activitat).

He fet un petit script que fa això fent servir el coeficient de Tanimoto (a partir dels fingerprints) per mesurar la semblança. El codi agafa les molècules query i les compara amb totes aquelles molècules de la base de dades on volem trobar molècules semblants (en l’exemple, els fàrmacs). Finalment, n’extreu aquelles parelles que estan dintre d’uns límits de semblança definits (éssent el coeficient 1 per dues molècules iguals i 0 per dues molècules completament diferents). Els resultats, les parelles de molècules, es desen en un sd file on s’ha afegint un camp relatiu a la semblança.

El codi està desenvolupat amb python fent ús de les llibreries de pybel. La crida del codi és ben senzilla, simplement cal indicar-li el fitxer amb les molècules query, el fitxer amb les molècules de referència i el límit de semblança (predefinit a 0.9).

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python SimMolecules.py -i query.sdf -d db.sdf

A continuació teniu el codi:

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"""
SimMolecules, a script to compare two molecular databases
Alfons Nonell-Canals - July 2010
"""
 
import fileinput
from pybel import *
import optparse
 
p = optparse.OptionParser()
p.add_option('--DBFile', '-d', default='0', help='Database of molecules used as a reference')
p.add_option('--sdf','-i',default='0', help='File with the query molecules')
p.add_option('--CutOff','-c',default='0.9', help = 'Similarity CutOff.')
options, arguments = p.parse_args()
 
#Read commandline options
db = options.DBFile
input= options.sdf
cutOff = float(options.CutOff)
 
RefDbfp = {}
RefDbmols = {}
 
for mol in readfile('sdf',db):
    fp = mol.calcfp()
    RefDbfp[mol.title] = fp
    RefDbmols[mol.title] = mol
 
for mol in readfile('sdf',input):
    fp = mol.calcfp()
    for RefMol in RefDbfp:
        tanimoto = fp|RefDbfp[RefMol]
        if tanimoto >= cutOff:
            print mol.title, RefMol, tanimoto
            mol.data['Similarity'] = tanimoto
            outRef = input.replace('sdf','Refs.sdf')
            out = open(outRef,'a')
            out.write(mol.write('sdf'))
            RefMolMol = RefDbmols[RefMol]
            out.write(RefMolMol.write('sdf'))
            out.close()