Sunday, 8 March 2015

GPMDB identifications by Original source


Tuesday, 20 January 2015

Bioinformatics for Proteomics Course, Bergen, April 21-24th 2015

The course will include lectures and practicals on open access software for the analysis of mass spectrometry generated proteomics data. Among the tools covering both protein identification and quantification are: SearchGUI, PeptideShaker, MaxQuant, Perseus and Skyline.
Topics Covered:
Why is the experimental design important? What is a protein database? How to convert raw mass spectrometry data to the required formats? What is a proteomics search engine and how do they work? What is protein inference and why is it important? How to interpret and validate proteomics results? What is functional analysis of proteomics data? How to share and reprocess proteomics data? How to quantify proteins?
Special Guest Lecture:
"Introduction to mass spectrometry based proteomics" by Prof. Dr. Lennart Martens from Ghent University and VIB, Ghent, Belgium.

For more details and registration please see the course details.

Monday, 5 January 2015

It's impossible to conduct research without software, say 7 out of 10 UK researchers

By Simon Hettrick, Deputy Director. Originally posted in SSI

No one knows how much software is used in research. Look around any lab and you’ll see software – both standard and bespoke – being used by all disciplines and seniorities of researchers. Software is clearly fundamental to research, but we can’t prove this without evidence. And this lack of evidence is the reason why we ran a survey of researchers at 15 Russell Group universities to find out about their software use and background.

Headline figures

  • 92% of academics use research software
  • 69% say that their research would not be practical without it
  • 56% develop their own software (worryingly, 21% of those have no training in software development
  • 70% of male researchers develop their own software, and only 30% of female researchers do so

Friday, 2 January 2015

Brazil: A place for Science and Friendship

It's really difficult to break stereotypes, especially for developing countries, like Brazil. If you mention its name around the world they are immediately associated with: sports, music, beaches, rum and "País do Carnaval". If you ask to someone in the streets of Germany or China about personalities from Brazil, they will mention Pelé. Breaking stereotypes is a task for years or centuries but we are going in the right direction.

Hotel Ferradura/ Ferradura Resort
Last December I attended to the 2nd Proteomics Meeting of the Brazilian Proteomics Society jointly with the 2nd Pan American HUPO Meeting in Hotel Ferradura/ Ferradura Resort, Búzios, Rio de Janeiro State, Brazil. The venue was gorgeous, mountains close to a small bay that offers calm, clear waters and the open sea. We arrived after 2 hours by car from Rio international airport. My plans, give a talk about PRIDE and ProteomeXchange but more than that, my talk was about "if we really need to share our proteomics data".  

Thursday, 1 January 2015

Trends in Mass Spec Instruments

I'm not doing marketing for any of the mass spec producers. Here a recently statistic I got about the use of different mass spec instruments using the public data in PRIDE Archive. It can help to researcher to eveluate which are the most popular and well-stablished instruments. 

Happy New Year!!!

Tuesday, 25 November 2014

HUPO-PSI Meeting 2014: Rookie’s Notes

Standardisation: the most difficult flower to grow.
The PSI (Proteomics Standard Initiative) 2014 Meeting was held this year in Frankfurt (13-17 of April) and I can say I’m now part of this history. First, I will try to describe with a couple of sentences (for sure I will fai) the incredible venue, the Schloss Reinhartshausen Kempinski. When I saw for the first time the hotel, first thing came to my mind was those films from the 50s. Everything was elegant, classic, sophisticated - from the decoration to a small latch. The food was incredible and the service is first class from the moment you set foot on the front step and throughout the whole stay. 
Standardization is the process of developing and implementing technical standards. Standardization can help to maximize compatibility, interoperability, safety, repeatability, or quality. It can also facilitate commoditization of formerly custom processes. In bioinformatics, the standardization of file formats, vocabulary, and resources is a job that all of us appreciate but for several reasons nobody wants to do. First of all, standardization in bioinformatics means that you need to organize and merge different experimental and in-silico pipelines to have a common way to represent the information. In proteomics for example, you can use different sample preparation, combined with different fractionation techniques and different mass spectrometers; and finally using different search engines and post-processing tools. The diversity and possible combinations is needed because allow to explore different solutions for complex problems. (Standarization in Proteomics: From raw data to metadata files).