Tune up your pipeline with Luigi, the Python module to manage workflow used in Spotify.

Yesterday I have found an amazing audio comment on Nature's Arts and Books blog that was discussing a possible influence of music on the development of modern science. Among the many connections we may find between science and music, the one I am going to propose today turns out quite unexpected. I understand that pipeline development is … Continue reading Tune up your pipeline with Luigi, the Python module to manage workflow used in Spotify.

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The Oncodrive suite. Bionformatics methods to detect driver mutations in cancer.

One of the most amazing groups whose work I have recently explored, is based in the rapidly- growing young UPF university in Barcelona. The Biomedical Genomics Group applies its high computational expertise to cancer research, focusing on the identification of those mutations that are actually involved in determining the tumor phenotype, the so- called driver mutations. The … Continue reading The Oncodrive suite. Bionformatics methods to detect driver mutations in cancer.

Software Carpentry. A great resource to learn scientific computing.

Software Carpentry is a volunteer organization founded in 1998, whose mission is to enhance scientists' productivity by teaching them basic computer skills. From January 2012, Software Carpentry joined the Mozilla galaxy, to become part of Mozilla Science Lab in June 2013. The organization provides workshops in several parts of the word and free online lessons. Their … Continue reading Software Carpentry. A great resource to learn scientific computing.

Dealing with Uniprot- Python programming interface.

My thesis is mostly focused on proteins, and be sure that I got really familiar with Uniprot. Uniprot comes out with a strong user interface that ease any approach. Biochemists can easily find what they need as a bioinformatician can set up his scripts to obtain information directly from the database. In fact, Uniprot has … Continue reading Dealing with Uniprot- Python programming interface.

PANDAS creator explains how to move the very first steps in Python data analysis.

The very first thing that comes to mind when the words statistics and programming are associated is definetly R. The R language represents the most used coding language in statistics and data analysis. But, what if you had to embedd the statistic part of your work in a bigger scripting project? What if you need … Continue reading PANDAS creator explains how to move the very first steps in Python data analysis.

PyMOD, a PyMol plugin for embedding multiple alignments in homology modelling

The project I want to discuss today is probably the best thing that came out from my actual lab in the latest years (Bioinformatics Lab at Biochemistry Department of Sapienza University of Rome). Carried on by Emanuele Bramucci for his Master thesis, PyMOD is a plugin for the famous molecular visualization system PyMol and it … Continue reading PyMOD, a PyMol plugin for embedding multiple alignments in homology modelling

Introducing pyphylogenomics 0.2.0, a python module for phylogenomics.

If we have to find a word to best represent the encounter between informatics and evolutionary biology, that word would definitely be phylogenomics. The large-scale analysis, allowed by the big amount of data made available in the last 20 years, is rapidly imposing the rule that "nothing makes sense in evolutionary biology except in the … Continue reading Introducing pyphylogenomics 0.2.0, a python module for phylogenomics.