Marco Brandizi's Site

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Presepi crociati, riassunto delle puntate precedenti [Italian]

[Presepe di migranti sui barconi]Scusate, ma quale casa nostra?! Io, come qualche altro milione di italiani, da ‘casa nostra’ sono stato spinto a fuggire, e non ho molte speranze di tornarci, a ‘casa nostra’. Casa nostra, quale? Quella nella quale gli inquilini rubano 150 miliardi di euro l’anno dalla cassa comune, sotto forma di evasione fiscale? Oppure quella in cui si costruisce sul greto dei fiumi e si getta la monnezza in giro per i campi, fottendosene della legge e degli altri padroni a casa nostra, attendendo l’ennesimo condono che sarà l’ultimo, e facendo i piagnoni alla piove-governo-ladro, quando si scopre che, pensa un po’, se diluvia, il fiume ti allaga casa, e non glie ne frega niente di te che vuoi fare il padrone scellerato a casa tua. Oppure, padroni di educare i figli con le peggio cose da strapaese, mandandoli a scuola con la carta da cesso nello zaino, insegnandogli la tradizione del presepe, mentre si nega il pranzo ai figli di chi non riesce a pagare la quota mensa? E poi, Rozzano casa nostra?! Ma se di Rozzano non è mai fregato una mazza a nessuno, e quando dici Rozzano, magari parlando degli eroi che da quelle parti si occupano del sociale e fanno volontariato, ai più vengono in mente solo i casermoni, i quartieri dormitorio, dove vivono gli sfigati, porta a porta con mafiosi e terroni.

Due o tre cose che so dell'iPhone (e Renzi probabilmente no) [Italian]

[Gettoni d'oro Canale 5]D’accordo, d'accordo, è ideologia, è roba vecchia, di gente che, come ricorda Riccardo Luna, si vantava di non usare il cellulare. Vogliamo fare una lettura ‘moderna’ del mito dell’iPhone? Uno compra questo gingillo da 7-800 euro e poi è la casa madre che decide cosa ci può fare o non fare. E’ il modello dell’AppStore. Io negli anni 90, quando Renzi metteva da parte i gettoni della Ruota della Fortuna, leggevo cose come The Cathedral and the Bazaar, o la rivista della Shake edizioni. Erano letture molto appassionanti, perché la Sinistra entrava dentro la rivoluzione digitale, mettendo in discussione i monopoli, la distribuzione della e l’accesso alla proprietà intellettuale, la libertà di usare la tecnologia, senza esserne usati.

A Geek's Intro to Linked Open Data

I've had a chance to give this tutorial about Linked Open Data. It was at /dev/summer/2014, a very nice 1-day meeting, packed with a great variety of topics for software developers. It was very nice to go around the presentation rooms and get a bite of so many new topics.

I've adapted the material from a similar, longer tutorial.

Lunch Break during /dev/summer/2014

Linked Open Data @SOD 2014

Me during SOD PresentationI haven't had much time recently to update this personal web site, I realise it seems abandoned. Well, the good news is that what I've been busy with is cool! :-)
 

For instance, end of March, I enjoyed working with my Italian friends from the Spaghetti Open Data Group, to deliver a 1-day tutorial on Linked Data and their applications for the cause of Open Data to the People! I was very happy of the people I worked with, they was great in providing a comprehensive presentation of different aspects of Linked Data essentials and why they're important for making data available to people in their most useful form.

There is a Google Doc, containing all the links to the materials we used that day, including presentations, demo and exercise data-to-RDF projects.

I've partiallty reused such material to prepare a much shorter presentation, going to talk about this here.

 

The EBI RDF Platform: Linked Open Data for the Life Sciences.

Jupp, S., J. Malone, J. Bolleman, M. Brandizi, M. Davies, L. Garcia, A. Gaulton, S. Gehant, C. Laibe, N. Redaschi, et al., "The EBI RDF Platform: Linked Open Data for the Life Sciences.", Bioinformatics, 2014 Jan 11.

MOTIVATION: RDF is an emerging technology for describing, publishing and linking life science data. As a major provider of bioinformatics data and services, the European Bioinformatics Institute (EBI) is committed to making data readily accessible to the community in ways that meet existing demand. The EBI RDF platform has been developed to meet an increasing demand to coordinate RDF activities across the institute and provides a new entry point to querying and exploring integrated resources available at the EBI.

AVAILABILITY: http://www.ebi.ac.uk/rdf.

Fate un favore ai Vostri ragazzi, non offrite una cattedra a Vannoni [Italian]

Cambridge (UK), 19/11/2013

A: Preside del liceo 'Mattioli' di Vasto, rappresentanti dei genitori, studenti, a chiunque vorrà leggere questa lettera aperta

Oggetto: Fate un favore ai Vostri ragazzi, non offrite una cattedra a Vannoni

Gentili Signori,

chi vi scrive (di getto) non è nessuno. Solo un anonimo cittadino, che cerca di informarsi su come va il mondo e, in questo mondo, di viverci, pensando anche agli altri e non esclusivamente pensando agli affari propri. Sono anche uno sviluppatore software, lavoro e conduco ricerca applicata nel campo della bioinformatica, che si occupa di far avanzare la biologia e la medicina con i computer. Deve essere per questo mio lavoro che mi ha molto colpito la notizia [1] che il vostro liceo sta per ospitare una conferenza del dottor Davide Vannoni, esperto in psicologia e comunicazione, recentemente assurto alla ribalta della cronaca, grazie ad una incredibile battaglia mediatica, capitanata dalla trasmissione 'Le Iene' e chissà da quanti altri dietro le quinte, che si sono assunti la responsabilità di porre la salute delle persone sotto i riflettori e trasformarla in una questione di tifoseria.

Open Data during the G8 Week: the SEMIC 2013 Conference

[Dublin Rugby Stadium, SEMIC 2013 Venue]

A few notes from the SEMIC 2013 conference that I've recent attended, which happended the same days of the Open Data Charts release, by the G8.

A few notes from UK Ontology Network 2013

[UK Ontology Network]

A few notes here about the UK Ontology Network Meeting I've attended today. PDF available too.

[Cover]
As their site says:

The UK Ontology Network is an informal and voluntary coordination between people based in the United Kingdom and working in the area of ontology and ontology related technology. Members of the network include people from all areas of science and industry and across all disciplines.

It has been nice to see works in a variety of fields, where clearly there are different approaches and philosopies on designing and applying ontologies.

 

 

Happy Releases with Maven and Bamboo

[Dilbert on Software Versions, courtesy of dilbert.com]
Maven has several nice plug-ins to automate almost all the stages of a release process. Whether it is changing your POM with a new version number, tagging your SCM or updating references in other POMs, you can do it by just a few command lines. Even better, you can put Maven goals into a continuous integration software and release with just a few clicks.

ArrayExpress update--trends in database growth and links to data analysis tools.

Rustici, G., N. Kolesnikov, M. Brandizi, T. Burdett, M. Dylag, I. Emam, A. Farne, E. Hastings, J. Ison, M. Keays, et al., "ArrayExpress update--trends in database growth and links to data analysis tools.", Nucleic Acids Res, 2012 Nov 27.

The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one of three international functional genomics public data repositories, alongside the Gene Expression Omnibus at NCBI and the DDBJ Omics Archive, supporting peer-reviewed publications. It accepts data generated by sequencing or array-based technologies and currently contains data from almost a million assays, from over 30 000 experiments. The proportion of sequencing-based submissions has grown significantly over the last 2 years and has reached, in 2012, 15% of all new data. All data are available from ArrayExpress in MAGE-TAB format, which allows robust linking to data analysis and visualization tools, including Bioconductor and GenomeSpace. Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data.

Cambridge after rain

Every Programmer has its Own Toolbox: jUtils

[Young Worker With his Toolbox - courtesy of http://www.joli-petite.com]My personal lib of utils is now a quite public project, jUtils (part of ISA-Tools) and the code in it doesn't come from myself only any more. In this post, I'd like to give a brief overview of what it offers. Who knows, that bit you were about to code yourself might be described in the next paragraphs.

graph2tab, a library to convert experimental workflow graphs into tabular formats.

Brandizi, M., N. Kurbatova, U. Sarkans, and P. Rocca-Serra, "graph2tab, a library to convert experimental workflow graphs into tabular formats.", Bioinformatics, 2012 May 3.

[graph2tab]

Motivations: Spreadsheet-like tabular formats are ever more popular in the biomedical field as a mean for experimental reporting. The problem of converting the graph of an experimental workflow into a table-based representation occurs in many such formats and is not easy to solve.

Results: We describe graph2tab, a library that implements methods to realise such a conversion in a size-optimised way. Our solution is generic and can be adapted to specific cases of data exporters or data converters that need to be implemented.

Availability and Implementation: The library source code and documentation are available at http://github.com/ISA-tools/graph2tab.

Contact: brandizi@ebi.ac.uk.

Supplementary Information: A supplementary document describes the theoretical and technical details about the library implementation.

The BioSample Database (BioSD) at the European Bioinformatics Institute.

Gostev, M., A. Faulconbridge, M. Brandizi, J. Fernandez-Banet, U. Sarkans, A. Brazma, and H. Parkinson, "The BioSample Database (BioSD) at the European Bioinformatics Institute.", Nucleic Acids Res, vol. 40, issue Database issue, pp. D64-70, 2012 Jan.

The BioSample Database is a new database at EBI that stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. The goals of the BioSample Database include: (i) recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE; (ii) minimizing data entry efforts for EBI database submitters by enabling submitting sample descriptions once and referencing them later in data submissions to assay databases and (iii) supporting cross database queries by sample characteristics. Each sample in the database is assigned an accession number.

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