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| ====== Bioinformatics Nano Course ====== | ====== Bioinformatics Nano Course ====== | ||
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| 1. **Dates**: 22-24 Mar 2010\\ | 1. **Dates**: 22-24 Mar 2010\\ | ||
| 2. **Name**: Bioinformatics: What? When? How?\\ | 2. **Name**: Bioinformatics: What? When? How?\\ | ||
| 3. **Description**: This nano course aims to answer three major questions about Bioinformatics: What is Bioinformatics? When should we consider a Bioinformatics approach? And how can Bioinformatics help us in a specific field of molecular biology?. To accomplish this goal, a series of lectures on different fields of Bioinformatics will be presented, in areas ranging from biologically relevant Databases to methods of High-throughput Genomics. We will present the current state of the art and what are the future perspectives, challenges and goals in the field. | 3. **Description**: This nano course aims to answer three major questions about Bioinformatics: What is Bioinformatics? When should we consider a Bioinformatics approach? And how can Bioinformatics help us in a specific field of molecular biology?. To accomplish this goal, a series of lectures on different fields of Bioinformatics will be presented, in areas ranging from biologically relevant Databases to methods of High-throughput Genomics. We will present the current state of the art and what are the future perspectives, challenges and goals in the field. | ||
| ==== Course Program ==== | ==== Course Program ==== | ||
| - | This course will consist in a series of talks followed by short journal clubs where groups of students will present papers suggested by the speakers of the previews talks.\\ | + | This course is part of IMM PhD Programme (http://www.imm.fm.ul.pt/web/imm/phdprogrammetraining) |
| - | The students need to prepare a 15-20 mins presentation about the paper (5 powerpoint slides maximum, can be prepared to guide the presentation), presenting the general idea of the paper, by explaining the problem, describing what methods were used, and what were the article main achievements. | + | It will consist in a series of talks followed by short journal clubs where groups of students will present papers suggested by the speakers of the previews talks.\\ |
| + | The groups for the journal club preparation will be posted soon.\\ | ||
| + | The students need to prepare a 15-20 mins presentation about the paper (5 powerpoint slides maximum, can be prepared to guide the presentation), presenting the general idea of the paper, by explaining the problem, describing what methods were used, and what were the article main achievements.\\ | ||
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| + | All the course talks will be on **room 51** floor 0 of EEM building for Monday and Wednesday. The Tuesday classes will be on **room 52**. \\The only exception will be David Aanansen's talk, that is scheduled to **room 57**, since it is a IMM seminar. | ||
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| ^ Monday 22 ^ Speaker ^ Title ^ Paper ^ | ^ Monday 22 ^ Speaker ^ Title ^ Paper ^ | ||
| - | | 9:00 - 10:00 | Pedro Fernandes | Data resources for Biomedical usage | 1) {{:courses:1_brooksbank_nucleic_acids_research_2010.pdf|}} | | + | | 9:00 - 10:00 | [[http://pt.linkedin.com/in/pedrofernandesbioinformatics|Pedro Fernandes]] ([[http://gtpb.igc.gulbenkian.pt/bicourses/|GTBC]],[[http://hermes.igc.gulbenkian.pt/|Hermes]]) | Data resources for Biomedical usage | 1) {{:courses:1_brooksbank_nucleic_acids_research_2010.pdf|}} | |
| - | | 10:00 - 11:00 | Ana Teresa Freitas | Biological Sequence Analysis | 2) {{:courses:2_pertsemlidis_genome_biol_2001.pdf|}} | | + | | 10:00 - 11:00 | [[http://kdbio.inesc-id.pt/~atf/ |Ana Teresa Freitas]] | Biological Sequence Analysis | 2) {{:courses:2_pertsemlidis_genome_biol_2001.pdf|}} | |
| - | | 11:00 - 12:00 | //Journal Club// 1)+2) ||| | + | | 11h00 - 12h00 | //Journal Club// 1)+2) ||| |
| - | | 12:00 - 13:00 | David Aanansen | The use and development of web applications for infectious disease microbiology | 3) {{:courses:3_grundmann_plos_med_2010.pdf|}} | | + | | 12h00 - 13h00 | [[http://www1.imperial.ac.uk/medicine/people/d.aanensen/ | David Aanensen]] | The use and development of web applications for infectious disease microbiology | 3) {{:courses:3_grundmann_plos_med_2010.pdf|}} | |
| - | | 13:00 - 14:30 | Lunch ||| | + | | 13h00 - 14h30 | Lunch ||| |
| - | | 14h30 - 15h30 | João André Carriço | Epidemiological Data Integration, Visualization and Analysis: from databases to population genetics | 4) {{:courses:4_francisco_bmc_bioinformatics_2009.pdf|}} | | + | | 14h30 - 15h30 | [[http://www.joaocarrico.info|João André Carriço]] | Epidemiological Data Integration, Visualization and Analysis: from databases to population genetics | 4) {{:courses:4_francisco_bmc_bioinformatics_2009.pdf|}} | |
| - | | 15h30 - 16h30 | Francisco Couto | Untangling BioOntologies for Effectively Exploring Biomedical Information | 5) {{:courses:5_pesquita_ploscompbiol_2009.pdf|}} | | + | | 15h30 - 16h30 | [[http://homepages.di.fc.ul.pt/~fjmc/|Francisco Couto]] | Untangling BioOntologies for Effectively Exploring Biomedical Information | 5) {{:courses:5_pesquita_ploscompbiol_2009.pdf|}} | |
| - | | 16h30 - 18h00 | //Journal Club// 6)+7) ||| | + | | 16h30 - 18h00 | //Journal Club// 3)+4)+5) ||| |
| + | \\ | ||
| + | \\ | ||
| ^ Tuesday 23 ^ Speaker ^ Title ^ Paper ^ | ^ Tuesday 23 ^ Speaker ^ Title ^ Paper ^ | ||
| - | | 14:00 - 15:00 | Francisco Pinto | Topology-function relations in regulatory networks | 6) {{:courses:6_milo_science_2002.pdf|}} | | + | | 14h00 - 15h00 | [[http://www.dqb.fc.ul.pt/docentes/frpinto/|Francisco Pinto]] | Topology-function relations in regulatory networks | 6) {{:courses:6_milo_science_2002.pdf|}} | |
| - | | 15:00 - 16:00 | Sara Mandeira | An overview on heterogeneous data integration in biology and medicine | 7) {{{:courses:7_huttenhower_genome_research_2009.pdf|}} | | + | | 15h00 - 16h00 | [[https://fenix.ist.utl.pt:443/homepage/ist46399|Sara Madeira]] | An overview on heterogeneous data integration in biology and medicine | 7) {{{:courses:7_huttenhower_genome_research_2009.pdf|}} | |
| - | | 16h15 - 18h00 | //Journal Club// 3)+4)+5) ||| | + | | 16h15 - 18h00 | //Journal Club// 6)+7) ||| |
| - | <html> | + | \\ |
| - | <Table border=1> | + | \\ |
| - | <TR><TH> </TH><TH>Mon 22</TH><TH>Tue 23</TH><TH>Wed 24</TH></TR> | + | ^ Wednesday 24 ^ Speaker ^ Title ^ Paper ^ |
| - | <TR><TH>9.00-10.00</TH><TD>Pedro Fernandes<BR><B>Data resources for Biomedical usage</B></TD><TD></TD><TD>Claudine Chaouiya<br><B>Qualitative modelling provides insights into the functioning of large biological regulatory networks</B></TD></TR> | + | | 9h00 - 10h00 | [[http://compbio.igc.gulbenkian.pt/nmd/node/14|Claudine Chaouiya]] | Qualitative modelling provides insights into the functioning of large biological regulatory networks | 8) {{:courses:8_samaga_plos_comput_biol_2009.pdf|}} | |
| - | <TR><TH>10.00-11.00</TH><TD>Ana Teresa Freitas<BR><b>Biological Sequence Analysis</b></TD><TD></TD><TD>Jorge Carneiro<br><b>Towards the automated analysis of living cells and tissues based on morphodynamic models</b></TD></TR> | + | | 10h00 - 11h00 | [[http://eao.igc.gulbenkian.pt/ti/Gente/Jorge/|Jorge Carneiro]] | Towards the automated analysis of living cells and tissues based on morphodynamic models | 9) {{:courses:9_farhadifar_curr_biol_2007.pdf|}} | |
| - | <TR><TH>11.00-12.00</TH><TD><b>--JC--</b></TD><TD><b></b></TD><TD><b>--JC--</b></TD></TR> | + | | 11h00 - 12h00 | //Journal Club// 8)+9) ||| |
| - | <TR><TH>12.00-13.00</TH><TD><I>IMM Seminar</I> - David Aanansen<br><b>The use and development of web applications for infectious disease microbiology</b></TD><TD><I>LUNCH - Pizza Seminar</I></TD><TD><I>LUNCH</I></TD></TR> | + | | 12h00 - 14h00 | Lunch ||| |
| - | <TR><TH>13.00-14.00</TH><TD><I>LUNCH</I></TD><TD><I>LUNCH</I></TD><TD><I>LUNCH</I></TD></TR> | + | | 14h00 - 15h00 | [[http://biopseg.deb.uminho.pt/irocha/|Isabel Rocha]] | Metabolic Systems Biology | 10) {{:courses:10_chavali_mol_syst_biol_2008.pdf|}} | |
| - | <TR><TH>14.00-15.00</TH><TD>(14h30) João A Carriço <br><b>Epidemiological Data Integration, Visualization and Analysis: from databases to population genetics</b></TD><TD>Francisco Pinto<br><b>Topology-function relations in regulatory networks</b></TD><TD>Isabel Rocha<BR><B>Metabolic Systems Biology</B></TD></TR> | + | | 15h00 - 16h00 | [[http://sbd.itqb.unl.pt/Site/Home.html|Andreas Bohn]] | Computing microbial biofilms: a case for ecological informatics | 11) {{:courses:11_jones_annu_rev_ecol_evol_sys_2008.pdf|}} | |
| - | <TR><TH>15.00-16.00</TH><TD>(15:30)Francisco Couto <br> <b>Untangling BioOntologies for Effectively Exploring Biomedical Information</b></TD><TD>Sara Madeira<br><b>An overview on heterogeneous data integration in biology and medicine</b></TD><TD>Andreas Bohn<br><b> Computing microbial biofilms: a case for ecological informatics</b></TD></TR> | + | | 16h15 - 18h00 | //Journal Club// 10)+11) ||| |
| - | <TR><TH>16.00-17.00</TH><TD><b>--JC--</b></TD><TD><b>--JC--</b></TD><TD><b>--JC--</b></TD></TR> | + | |
| - | <TR><TH>17.00-18.00</TH><TD><b>--JC--</b></TD><TD><b>--JC--</b></TD><TD><b>--JC--</b></TD></TR> | + | |
| + | ==== Journal Club Articles ==== | ||
| - | </Table> | + | [[courses:bioinformatics:articles| Click here for Journal Club Article keywords ]] |
| - | </html> | + | |