organisation - the Instituto Gulbenkian de Ciência

BIOINFORMATICS
AND COMPUTATIONAL
BIOLOGY UNIT
José Pereira Leal Head
PhD in Biomedical Sciences, Universidade do Porto, Portugal, 2001
PI of Computational Genomics Group
Head of Facility since 2006
link to unit website
The unit´s mission is to promote the use of computational methods in biological
research, through training and development of resources and materials:
• Support the graduate programmes of the Oeiras Associated Laboratory (LAO);
• Provide technical and scientific direct user support in biological data analysis
using computational methods;
• Conduct research and development in bioinformatics, in particular in dataflow,
data warehousing and data analysis, supporting the LAO;
• Provide a computing infrastructure suited for biocomputing;
• Collaborate with middle and high schools producing bioinformatics activities
and introducing teachers and students to new methods of learning
biology.
FACILITY STAFF
Maria Isabel Marques (Senior Bioinformatics Specialist)
Paulo Almeida (Systems administrator & Programmer)
Renato Alves (Systems administrator & Programmer)
Isabel Neves (Researcher)
Patrícia Soares (Programmer)
PUBLIC ENGAGEMENT IN SCIENCE
Talks for school students (Loures)
Seminars for high-school teachers, Biology in Modern Times series, IGC, July
Teacher training in bioinformatics, January, February
MAJOR PROJECTS AND ACCOMPLISHMENTS
• inTB: Collaborative project with the Collective Dynamics group (IGC) and the
Genomics Facility (IGC) on an FCT grant designed to establish a molecular
framework for the study of epidemiology of tuberculosis in Portugal. We
have developed and implemented a new web-based database and on-line
analysis tool to support this project, the inTB: Integrating Clinical Demographic
and Molecular Data in Tuberculosis. Two papers are in production;
• CorkoakDB: A collaborative project with several groups at the Oeiras Associated
Laboratory, on an FCT grant for the sequencing of the ESTs of
the cork oak, in response to a call by Government. During this year, an
assembly and annotation pipeline was finished and a web application was
developed to present all the information to collaborators and eventually a
wider audience. Two papers are in production;
• FlowBase: Data warehousing environment for flow cytometry experiments.
We developed and implemented the whole system, which has been submitted
for publication. Other warehousing solutions are maintained in the unit
for microarray data;
• MTOC-explorer: We collaborate with the Computational Genomics Laboratory
(IGC) and Cell Cycle Regulation (IGC) in MTOC-explorer, a bioinformatics
resource that allows integrating morphological information from microscopy
images with genomic information. Images are annotated and curated by an
international team of domain experts in a broad range of eukaryotes using
a controlled vocabulary developed specifically for this task. By centralising
this knowledge, and using a controlled vocabulary, the resulting collection
of images can be mined in a way which is not possible when knowledge is
dispersed. At the moment, the database contains over 500 images from 100
species in all major eukaryotic branches. One paper is in production.
• Technical and scientific direct-user support: Eighteen IGC groups, seven
IGC-associated groups and five non IGC groups received extensive technical
and scientific support, including: Assembly (Staden); finding copy number
variation; SNP analysis; finding mutations; browsing genomes, finding genes,
transcripts, proteins, SNPs, microRNAs; transcript identification, alignments,
RT-PCR primers; morpholino design; browsing the mtocdb to search
for gene orthologues/paralogues; transcription binding factors: Transfac,
Genomatix, Galaxy; searching for homologues-BLASTS: finding homologues,
orthologues and paralogues; finding and analysing protein families;
clustering proteins according to protein families: domain searching;
patterns searching; finding isoforms; Interpro and SuperFamily searching;
identifying and counting microRNAs in sequencing libraries; phylogenetic
analysis: Phylip, MrByes and Pymol; PhenomicDB database; Script design:
perl script for Blasting and parsing FASTA files; support in NGS analysis
data; script for DNA sequencing to automate the analysis; bioinformatics
software consulting. We contributed to the production of Master and PhD
Theses, papers, and scientific communications.
IGC ANNUAL REPORT ‘11
FACILITIES AND SERVICES
97