Sergio Contrino

Professional experience

September 06 – present 
CRS4-Centre for Advanced Studies, Research and Development in Sardinia, 
Bioinformatics group, Loc. Piscinamanna,  09010 Pula (CA), Italy.

Activities of support and educational regarding the use of databases and database applications in biology, both in the group and with the companies present in the scientific park. Development of a genotyping database. Set up of a database infrastructure for microarray experiments.

June 96 – June 05 
EBI-European Bioinformatics Institute,
Genome Campus, Hinxton, Cambs, U.K.

I have been involved in different projects in various fields of life science.

Microarray: since June 2002 I have worked with the Microarray informatics group. I have contributed to the development of a web based tool for on-line submission of gene expression data and to its specialised version for toxicological gene expression experiments [http://www.ebi.ac.uk/miamexpress/] (MySQL, Perl, CGI).

I have also helped setting up a data warehouse for easy query and analysis of the microarray data in our public repository [http://www.ebi.ac.uk/aedw/] (Oracle, Java, Servlets).

Protein data: from 1996 to 2002 I have worked extensively in the setting of public databases for protein data. In particular, I contributed to the creation of TrEMBL, a protein database automatically derived from the nucleotide EMBL database. I produced the first 4 releases of the database, formalised and documented the whole procedure, trained the new staff that took over the task (shell, C, python, awk).

I also developed a relational implementation of TrEMBL and its manually annotated counterpart Swiss-Prot, designing the relational schema of the database and providing programmatic access to it (Designer 2000, C++, ProC, SQL).

Nucleotide data: I was in charge of the cross-reference between the EMBL nucleotide database and other biological databases (SQL, SQL Loader, awk, PRO*C).

I was also involved in Oracle forms development and maintenance (Forms 4.5, PL/SQL) and some user support (Oracle webserver).

Human chromosome database : in cooperation with a curator, I set up a database of human genes and their locations, with links to many other sources of related information and a search engine (Oracle, SQL, Java, Servlets), that was used as a template for the access to the entire proteomic data of EBI.

Ontologies (Biological chemistry): together with a colleague, I have set up a relational database for an ontology of bioinorganic proteins (COMe), with search engine and graphical navigation of the ontology. [http://www.ebi.ac.uk/come] (Oracle, SQL, Java, Servlets).

Most of these projects or their documentation can still be accessed via my EBI home page [http://www.ebi.ac.uk/~contrino/].

June 93 - June 96
Sincrotrone S.C.p.A.,
Trieste, Italy.

I worked as an engineer in the control system of the beam lines of the synchrotron. My job consisted mainly on the definition of the requirements for the various lines, the configuration of the control system and its test. I was the administrator of the database (Oracle) and I developed various applications for a quick configuration of the system (SQLplus). My work involved a lot of interactions with the researchers in the various lines, and I developed an internet-based local information system, with the possibility of direct queries to the configuration database (GSQL, PRO*C, CGI, NCSA http). This is a very common approach now but was very innovative at the time (1995).

February 92 - June 93
Marconi Technical Institute,
Monfalcone, Gorizia, Italy.

Teacher (Automatic Systems and Electronics). I taught PASCAL and Assembler; we made some simple microprocessor circuit (using Z80).

Graduation thesis (Dec. 91)

It regarded air pollution control in urban area: a year-long collection of atmospheric and pollutant concentration data from a monitoring site in downtown Trieste was used for a series of statistical analysis.

April 89 - April 90
Santorio hospital, 
Trieste, Italy.

Military duties (civil service). Patients' assistant. I also ordered the archive and set a small library for the hospital patients.

January 88 - September 88
Volta Technical Institute, 
Trieste, Italy.

Teacher (Electrical Technology).


Technical skills and competencies

• Database technology (Oracle, MySQL): DBA, SQL, PL/SQL, PRO*C, JDBC, Servlets, Designer, Forms.
• Good software knowledge and practical experience on several programming languages (SQL, Java, C++, Perl, C, Python, Pascal, Assembler).
• Good experience with Unix and HTML publishing.
• Ontologies.
• Data mining.
• Statistics (multivariate analysis).
• System and control theory; Environmental matters.

Plus....

• External reviewer of applications for research funding.
• Currently attending a Diploma course in Archaeology at the University of Cambridge, Institute of Continuing Education.
• I have a keen interest in music and art in general. I play in various musical groups and I am a member of the Cambridge Jazz Cooperative.

Education

2006 Certificate in Enterprise, Centre for Entrepreneurial Learning, University of Cambridge.

1992 Qualified 'Ingegnere' (Engineer).

1991 Laurea, University of Trieste, Electronics Engineer (101/110)

Dissertation: "Air Pollution Control in Urban Area".

1982 Perito Industriale (technical A-level), "Volta", Trieste (45/60).

Diploma course in Archaeology, University of Cambridge, Institute of Continuing Education (part-time, started 2003).

Training and conferences

2007 “Management and analysis of Microarray data”, Sardegna Ricerche, Pula, Italy, Organiser.

2007 “Data and Text mining: from the web to biology”, Sardegna Ricerche, Pula, Italy, Organiser.

2006 Database workshop, Consorzio 21, Pula, Italy. Tutor.

2004 DESPRAD consortium (EU FP5) final meeting, Volterra, Italy. Organiser.

2004 “Microarray technology: genome - proteome – function”, EMBO course, Heidelberg. Tutor.

2004 “Oracle 9i: Program with PL/SQL”: Oracle University.

2003 “15th International school for Computer Science Researchers: Algorithmics for Data mining and Pattern Discovery”: Lipari Island

2002 “Standards and Ontologies for Functional Genomics (SOFG)” - Wellcome Trust, Hinxton, UK, paper on “Ontologies in Biological Chemistry”.

2001 “Mathematics and Computers in Biology and Chemistry 2001 (MCBC 2001)”, Skiathos Island, Greece, paper on “Exploring the Human Genome Date in SWISS-PROT and TrEMBL”.

2001 “Commodity Information Technologies for Bioinformatics” - BioStandards Workshop, EBI, Hinxton, UK: 14-15/05

2001 “XML” - BioStandards Workshop , EBI, Hinxton, UK: 26-28/02.

2000 "Advanced JAVA Programming" - BioStandards Workshop , EBI, Hinxton, UK: 27-28/11

2000 "Advanced CORBA Programming" - BioStandards Workshop , EBI, Hinxton, UK: 4-6/07.

2000 "CORBA programming" - BioStandards Workshop , EBI, Hinxton, UK: 26-28/01.
1999 “11th International school for Computer Science Researchers: Computational Biology”: Lipari Island.
1995 "Fuzzy logic in control systems: methods, software and applications"; Trieste 4-6/11.