Moderator: Giovanni M Dall'Olio

Reputation:
420
Status:
New User
Location:
Barcelona, Spain
Website:
http://bioinfoblog.it
Last seen:
8 years, 11 months ago
Joined:
10 years, 9 months ago
Email:
2*@lvh.me

PhD student at the Pompeu Fabra University in Barcelona. Interested in bioinformatics, R, python programming and agile techniques.

Posts by Giovanni M Dall'Olio

<prev • 16 results • page 1 of 2 • next >
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Answer: A: Computing The Reverse And Complement Of A Sequence With Biopython
... Wouldn't it better to have a single question titled 'How to compute the reverse complement with python' and put all the examples as different answers? Otherwise it seems a bit confusing.. ...
written 10.6 years ago by Giovanni M Dall'Olio420 • updated 10.6 years ago by User 82260
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Agile Programming For Bioinformaticians - Any Suggestions?
... I am planning to prepare a talk for my workmates, to introduce them the basics of some agile programming methodology, which I think could give us good ideas to improve our working as a team. My idea was to take inspiration from extreme programming and explain the rules I like the most: use of A7 ca ...
general agile good team written 10.6 years ago by Giovanni M Dall'Olio420 • updated 10.6 years ago by User 82260
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Answer: A: How To Organize A Pipeline Of Small Scripts Together?
... My favorite way of defining pipelines is by writing Makefiles, about which you can find a very good introduction in Software Carpentry for Bioinformatics: http://swc.scipy.org/lec/build.html . Although they have been originally developed for compiling programs, Makefiles allow to define which opera ...
written 10.7 years ago by Giovanni M Dall'Olio420 • updated 10.7 years ago by User 82260
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How To Organize A Pipeline Of Small Scripts Together?
... In bioinformatics it is very common to end up with a lot of small scripts, each one with a different scope - plotting a chart, converting a file into another format, execute small operations - so it is very important to have a good way to clue them together, to define which should be executed before ...
general make pipeline organization written 10.7 years ago by Giovanni M Dall'Olio420 • updated 10.6 years ago by User 82260
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Answer: A: Using Hdf5 To Store Bio-Data
... Unfortunately I don't have any example to shows you yet. I don't know how to program in C/C++ so I have been looking at two hdf5 wrappers in python, PyTables and H5PY. PyTables has a database-like approach in which HDF5 is used as a sort of hierarchical database, in which a column can be a table it ...
written 10.7 years ago by Giovanni M Dall'Olio420 • updated 10.7 years ago by User 82260
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What Is The Best Way To Share Scripts Between Members Of A Lab?
... One of the most awful problems in my group is avoiding to rewrite scripts that have been already written by others. Since we have different projects and we work with different data, everybody ends up writing its own scripts in his favorite programming language, and it is very frequent to waste an af ...
general subjective written 10.7 years ago by Giovanni M Dall'Olio420 • updated 10.7 years ago by User 82260
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How To Get The Sequence Of A Genomic Region From Ucsc?
... Let's say I want to download the fasta sequence of the region chr1:100000..200000 from the UCSC browser. How do you do that? I can't find a button to 'export to fasta' in the UCSC genome browser. I think that the solution is to click on one of the tracks displayed, but I am not sure of which. If I g ...
sequence ucsc fasta written 10.7 years ago by Giovanni M Dall'Olio420 • updated 10.7 years ago by Jane ♦♦ 0
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Where Can I Get The Secondary Structure Of A Protein?
... As in the title... I have a protein and I would like to know its secundary structure. I couldn't find it in uniprot, althought I tought they had annotations for it there. In the end I have used a predictor (jpred) but there it should be a database somewhere. ...
sequence protein structure written 10.7 years ago by Giovanni M Dall'Olio420 • updated 10.7 years ago by User 82260
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What Is Your Experience With The String (Interactions) Database?
... STRING is a database of predicted protein-protein interactions at EMBL. It cluster the results from many sources of protein-protein interactions databases, like Mint, etc.., and it also use the informations from KEGG-pathways and reactome, to provide the best annotations for the interactions of a pr ...
subjective string protein interacti ppi pin written 10.7 years ago by Giovanni M Dall'Olio420 • updated 10.6 years ago by Andrew Su0
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Answer: A: Which Are The Best Programming Languages To Study For A Bioinformatician?
... The choice of a programming language is purely subjective, but when a student asks you which programming language he should start with, you have to make an answer, or at least provide some informations. I think that a bioinformatician who studies R and at least two or three libraries (lattice/ggplo ...
written 10.7 years ago by Giovanni M Dall'Olio420 • updated 10.7 years ago by User 82260

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