organisation - the Instituto Gulbenkian de CiÃªncia

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EQUIPMENT AND INFRASTRUCTURE • Two Ion-Specific Probe (SIET) setups coupled with an inverted fluorescence microscope (Nikon). SIET is equipped with a IPA-2 Ion/Polarographic Amplifier and Computerised Motion Control (CMC-4), all from Applicable Electronics, LLC. A Hamamatsu Camera controller and an illumination system by Lambda DG-4 provide image acquisition. (Funding: Fundação para a Ciência e a Tecnologia, Portugal; Fundação Calouste Gulbenkian, Portugal); • ASIET setup coupled with a zoom scope imaging unit. The SIET comprises an IPA-2 Ion/Polarographic Amplifier and Computerised Motion Control (CMC-4), all from Applicable Electronics. (Funding: FP6 Network of Excellence "Cells into Organs", European Commission); • A Scanning Voltage Probe (SVET) coupled with an inverted microscope (Nikon) equipped with a Phase Sensitive Detector Amplifier - 2 channel (PSDA-2), a Computerized Motion Control (CMC-4), all from Applicable Electronics, LLC. A Minicamera UK-1117-M CCD ensures image acquisition. Funding Calouste Gulbenkian Foundation, Portugal IGC ANNUAL REPORT ‘11 FACILITIES AND SERVICES 96
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
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The Instituto Gulbenkian de Ciênci
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ORGANISATION CALOUSTE GULBENKIAN FO
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established a unique and diverse hu
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After all these years of a half-dis
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IGC ANNUAL REPORT ‘11 THE DIRECTO
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30 Nationalities working at the IGC
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2004 - 2011 NEW RESEARCH GRANTS BRE
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PROTEIN-NUCLEIC ACIDS INTERACTIONS
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MEIOSIS AND DEVELOPMENT Vítor Barb
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EPIGENETICS AND SOMA Vasco M. Barre
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VARIATION: DEVELOPMENT AND SELECTIO
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as a manuscript submitted in 2011 (
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We have found a new precursor struc
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We have previously developed a sper
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POPULATION AND CONSERVATION GENETIC
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NEUROBIOLOGY OF ACTION Rui M. Costa
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During this year we demonstrated th
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CELL BIOPHYSICS AND DEVELOPMENT Jos
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GENOME-WIDE ANALYSIS OF TELOMERE PR
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Improved ICT techniques and methodo
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ACTIN DYNAMICS Florence Janody Prin
Page 45 and 46: EPIGENETIC MECHANISMS Lars Jansen P
Page 47 and 48: SYSTEMS NEUROSCIENCE THIS GROUP IS
Page 49 and 50: PATTERNING AND MORPHOGENESIS Moisé
Page 51 and 52: EARLY FLY DEVELOPMENT Rui Gonçalo
Page 53 and 54: BEHAVIOURAL NEUROSCIENCE THIS GROUP
Page 55 and 56: DISEASE GENETICS Carlos Penha Gonç
Page 57 and 58: COMPUTATIONAL GENOMICS José Pereir
Page 59 and 60: COMPLEX ADAPTIVE SYSTEMS AND COMPUT
Page 61 and 62: hypothesis that expression of HO-1
Page 63 and 64: hemocyte purification using a combi
Page 65 and 66: EVOLUTIONARY GENETICS Henrique Teot
Page 67 and 68: BACTERIAL SIGNALLING Karina B. Xavi
Page 69 and 70: BIOPHYSICS AND GENETICS OF MORPHOGE
Page 71 and 72: PLANT GENOMICS Jörg Becker Researc
Page 73 and 74: NETWORK MODELLING Claudine Chaouiya
Page 75 and 76: NEURONAL STRUCTURE AND FUNCTION Inb
Page 77 and 78: NEUROETHOLOGY LABORATORY THIS GROUP
Page 79 and 80: LEARNING LABORATORY THIS GROUP IS A
Page 81 and 82: IMMUNE REGULATION Carlos E. Tadokor
Page 83 and 84: STRESS AND CYTOSKELETON Escola Supe
Page 85 and 86: ANIMAL FACILITIES Jocelyne Demengeo
Page 87 and 88: TRANSGENICS UNIT Moisés Mallo Head
Page 89 and 90: CELL IMAGING UNIT José Feijó Head
Page 91 and 92: GENOMICS UNIT Carlos Penha Gonçalv
Page 93 and 94: • Low noise (6 Rat arrays for Ins
Page 95: ION DYNAMICS FACILITY Ana Catarina
Page 99 and 100: PORTUGUESE BIOINFORMATICS CENTRE Pe
Page 101 and 102: INNOVATION AND TECHNOLOGY TRANSFER
Page 103 and 104: ADMINISTRATION AND ACCOUNTS José M
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Page 119 and 120: IGC ANNUAL REPORT ‘11 PUBLICATION
Page 121 and 122: António Coutinho Professional Meri
Page 123 and 124: GRADUATE TRAINING AND EDUCATION
Page 125 and 126: Cells to organisms I 24 - 28 Octobe
Page 127 and 128: INDP - INTERNATIONAL NEUROSCIENCE D
Page 129 and 130: Extroduction 30 May - 3 June Organi
Page 131 and 132: PROGRAMME FOR ADVANCED MEDICAL RESE
Page 133 and 134: GTPB - THE GULBENKIAN TRAINING PROG
Page 135 and 136: THESES MSc THESES Sofia Pereira Dev
Page 137 and 138: SEMINARS AT THE IGC JANUARY 2011 DA
Page 139 and 140: MARCH 2011 DATE SPEAKER AFFILIATION
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DECEMBER 2011 DATE SPEAKER AFFILIAT
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On the origin and diversification o
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HELENA COSTA Mechanism of IL-8 indu
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Of models and mechanisms of ion dyn
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The centromere: A showcase for epig
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Mechanisms determining adult body s
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The evolutionary dynamics of (Rab)
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HENRIQUE TEÓTONIO The genetic basi
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EMBnet - ANNUAL GENERAL MEETING 201
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PUBLIC ENGAGEMENT IN SCIENCE
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Science Projects Support Programme
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FUNDRAISING Maria João Leão Head
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PARTNERS AND SPONSORS Several partn
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