GTPB - the Gulbenkian Training Programme in Bioinformatics

Bioinformatics hands-on training in short face-to-face courses. GTPB provides skills in Bioinformatics through a simple but very effective methodology.

This page is a companion to
Hands-on Bioinformatics Training (open group)
https://www.facebook.com/group.php?gid=107472589301049
It documents GTPB courses, specifically. On a voluntary basis, course participants find each other.

Funcionando normalmente

GTPB: 3DAROC21 3C-based data analysis and 3D reconstruction of chromatin folding, 2021 - Home 13/09/2021

GTPB: 3DAROC21 3C-based data analysis and 3D reconstruction of chromatin folding, 2021 - Home

3DAROC21 Online Oct 4th-6th 2021
3C-based data analysis and 3D reconstruction of chromatin folding

http://gtpb.igc.gulbenkian.pt/bicourses/2021/3DAROC21/

3C-based methods, such as Hi-C, produce a huge amount of raw data as pairs of DNA reads that are in close spatial proximity in the cell nucleus. Overall, those interaction matrices have been used to study how the genome folds within the nucleus, which is one of the most fascinating problems in modern biology. The rigorous analysis of those paired-reads using computational tools has been essential to fully exploit the experimental technique, and to study how the genome is folded in space. Currently, there is a clear expansion on the wealth of data on genome structure with the availability of many datasets of Hi-C experiments down to 1Kb resolution (see for example:
http://hic.umassmed.edu/welcome/welcome.php or http://www.aidenlab.org/data.html).

In this course, participants will learn to use TADbit, a software designed and developed to manage all dimensionalities of the Hi-C data:

1D - Map paired-end sequences to generate Hi-C interaction matrices
2D - Normalize matrices and identify constitutive domains (TADs, compartments)
3D - Generate populations of structures which satisfy the Hi-C interaction matrices
4D - Compare samples at different time points

Participants can bring specific biological questions and/or their own 3C-based data to analyze during the course. At the end of the course, participants will be familiar with the TADbit software and will be able to fully analyze Hi-C data. Although the TADbit software is central in this course, alternative software will be discussed for each part of the analysis.

GTPB: 3DAROC21 3C-based data analysis and 3D reconstruction of chromatin folding, 2021 - Home Deadline for applications: th Course date: Oct 4th to Oct 6th 2021 Candidates with adequate profile will be accepted until we reach 20 participants. Decisions will be communicated by Sep 24th2021.

gtpb.igc.gulbenkian.pt 29/06/2020

GTPB Course Materials

Course material repositories, fully available for reuse (CC-BY 4.0), each provided with a website for easy navigation.
http://gtpb.igc.gulbenkian.pt/bicourses/Course_materials.html

gtpb.igc.gulbenkian.pt

figshare.com 10/06/2020

Collaborative development of training materials eases-up training course design and delivery.pdf

Collaborative development of training materials eases-up training course design and delivery

https://doi.org/10.6084/m9.figshare.12444161.v1

figshare.com In the preparation of a face-to-face training course, the instructors and organisers need to overcome a wide range of challenges. Often they come from geographically distant locations. This is one of the most common obstacles at the initial phase, and a motivation to use a collaborative set of softw...

[05/09/20]   Materials from 17 Bioinformatics Training courses, organised using the GTPB method, are now accessible via the Materials section of ElixirTeSS.
https://tess.elixir-europe.org/materials
For each course we share a website for easy navigation in the materials and the GitHub repository that generated it, thus enabling their reuse. Everything in Open Access, under CC-BY4.0 License. ElixirTeSS will make them much more findable.

23/01/2020

PSLS20 - Practical Statistics for the Life Sciences, 20 participants

10/04/2019

30 years of Bioinformatics training at the IGC

igc.gulbenkian.pt 10/04/2019

Media | Press releases | 2019

30 YEARS OF TRAINING IN BIOINFORMATICS IN PORTUGAL AT IGC
10-04-2019
On April 10, 1989, thirty years ago, David Philip Judge, collaborator of Martin Bishop at the University of Cambridge and a pioneer in the field, gave the first bioinformatics training class in Portugal at the Instituto Gulbenkian de Ciência (IGC).

David Judge was brought to the IGC by Nicolau van Uden, within the scope of the Master in Biotechnology organized with the New University of Lisbon, at a time when bioinformatics training didn't quite exist in Portugal.

Today, exactly 30 years later, we find David Judge at IGC to teach yet another class. In fact, Judge has been coming to IGC for the last 30 years, bringing with him not only the teaching and training techniques he has been developing and refining, but the example of extreme patience that is needed to meet the needs and doubts of the participants.

This year, the IGC also marks the twentieth year of the Gulbenkian Training Program in Bioinformatics (GTPB), whose roots are deeply rooted in this first training, and David Judge, the person who most contributed to the training in bioinformatics at IGC. The celebrations start today, the day the IGC marks the anniversary of Judge's first class.

igc.gulbenkian.pt

foster.gitbook.io 16/12/2018

Manual de Formação em Ciência Aberta - Manual de Formação em Ciência Aberta

FREE e-book, Open Science Training Handbook, translated in Portuguese https://foster.gitbook.io/manual-de-formacao-em-ciencia-aberta/

foster.gitbook.io Em fevereiro de 2018, um grupo de catorze autores reuniram-se na Biblioteca Nacional Alemã de Ciência e Tecnologia (Technische Informationsbibliothek - TIB), em Hanover, para criar um manual aberto e vivo sobre formação em Ciência Aberta. As formações de elevada qualidade são fundamentais qu...

27/10/2018

Instituto Gulbenkian de Ciência

O Instituto Gulbenkian de Ciência e a Universidade do Minho - Oficial lançaram a primeira versão digital do Manual de Formação em Ciência Aberta, destinada a formadores.

O manual resulta da tradução para Português do livro "Open Science Training Handbook". Pedro Fernandes, coordenador do GTPB - the Gulbenkian Training Programme in Bioinformatics do IGC é um dos autores da versão original e traduzida.

Esta contribuição surge na Semana Internacional da Ciência Aberta que termina no dia 28 de outubro.

17/09/2018

Starting the course by showing how to think in Biology using integrative methods in 3D, experimental, modelling, bioinformatics, etc.

[08/31/18]   If you have experienced attending a course in GTPB, either as a learner or as an instructor, please take a couple of minutes and file-in a Short Testimonial or a rating under "Reviews"

[08/31/18]   1006 Likes

[08/21/18]   Please rate our activity. We have lots of followers but we need you to rate us. In Facebook it is not really obvious that they now use the Review on the left had side menu.

gtpb.igc.gulbenkian.pt 03/08/2018

3DAROC18: 3C-based data analysis and 3D reconstruction of chromatin folding

http://gtpb.igc.gulbenkian.pt/bicourses/2018/3DAROC18/

gtpb.igc.gulbenkian.pt Deadline for applications: Aug 31st 2018 Course date: Sep 17th to Sept 21st 2018 Candidates with adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants.

[06/10/18]   The next course in GTPB will be a hands-on entry level course on programming (in Python). July 23-27. About to open for applications.

eracareers.pt 02/06/2018

eracareers

Scholarship available

A nice opportunity for someone wanting to have a fresh start at Bioinformatics Training provision.

Biodata-PT, the Portuguese national infrastructure for biomedical data, is selecting a Training Assistant to scale-up from the GTPB training model, and lay-out the plans to reproduce training at the country level. International connections, substantial learning in Bioinformatics and practice in training provision.

Training Assistant for Biodata.pt (recruiting)
http://www.eracareers.pt/opportunities/index.aspx?task=global&jobId=100246

Please help us to find the right person.
Open for applications from June 4th to June 15th

eracareers.pt The Instituto Gulbenkian de Ciência is welcoming applications for a Research Fellowship within the project 22231 with the title “Biodata.pt”, financed by FEDER, POCI, PORL, POA and national funds through FCT/MECTES (PIDDAC), with the following conditions:

02/06/2018

PDA18 - Proteomics Data Analysis @Instituto Gulbenkian de Ciência

[05/18/18]   PGDH18 - Population Genetics and Demographic Models training course ending today.

the-scientist.com 30/04/2018

Opinion: We Must Make Data More Accessible for Bioinformatics Training

https://www.the-scientist.com/?articles.view/articleNo/52085/title/Opinion--We-Must-Make-Data-More-Accessible-for-Bioinformatics-Training/

the-scientist.com In addition to programs geared towards transforming biologists into bioinformaticians, students need more raw material available for their education.

broadinstitute.org 25/04/2018

Broad Institute to sequence its 100,000th whole human genome on National DNA Day

Landmark!

broadinstitute.org Milestone to be crossed on the 15th anniversary of the completion of the Human Genome Project, as the worldwide estimate for whole human genomes sequenced approaches one million

23/02/2018

Entry Level Bioinformatics ended today, 12 more people attended

pic.twitter.com 18/02/2018

Richard Feynman on Twitter

We need to teach how doubt is not to be feared but welcomed and discussed. It's OK to say, "I don't know."

pic.twitter.com “We need to teach how doubt is not to be feared but welcomed and discussed. It's OK to say, "I don't know."”

[12/18/17]   2017 is ending. Maybe it is a good occasion to ask you to rate this resource with stars. Thank you for your support. Pedro Fernandes

21/10/2017

Four training courses open for applications right now. Check our website http://gtpb.igc.gulbenkian.pt

journals.plos.org 17/10/2017

Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience

Proud to have collaborated in this magnificent team.

journals.plos.org Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need o...

13/09/2017

IBSTATB17 Group Photos

[04/26/17]   ELB17F open for applications

20/04/2017

GTPB: ADER17 - Analysis of Differential Expression with RNAseq - Home

Today, 19 participants finished our hands-on RNAseq Bioinformatics Training course, GTPB's ADER17. http://gtpb.igc.gulbenkian.pt/bicourses/ADER17/

gtpb.igc.gulbenkian.pt IMPORTANT DATES for this Course Deadline for applications: April 10th 2017 Course dates: April 17th - April 20th 2017

17/03/2017

PGDH17 Group @ Palacio Marques de Pombal in Oeiras

17/03/2017

PGDH17 The group had a succesful course dinner @ Tasquinha da Vila in Paço de Arcos

[03/13/17]   PGDH17 - Population Genetics and Demographic History:
model-based approaches, has started today with 10 participants

[02/06/17]   GTPB - the Gulbenkian Training Programme in Bioinformatics

28/12/2016

IB16S - Introductory Bioinformatics, the second course of this type in 2016. In this course we received our participant number 5000.

03/12/2016

ELIXIR EXCELERATE Train-the-Trainer course in Ljubljana, with Allegra Via, Pedro Fernandes and Jure Dimec. 8 participants. The course included a real practical session with learners.

tonybates.ca 03/12/2016

How online learning is going to affect classroom design | Tony Bates

Getting inspired... The new Training Room at the IGC will be set for active learning and online delivery. To happen in 2017

tonybates.ca I have an unusual occupation. A couple of weeks ago I attended a meeting in an office furniture warehouse in a small industrial park in Vancouver. The purpose of the meeting? To explore how online learning is going to change the design of campus classrooms.

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30 years of Bioinformatics training at the IGC
Randomize and Explain, BPB12

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Crescendo Escola de Música Oeiras Crescendo Escola de Música Oeiras
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A Next Generation tem como objetivo proporcionar às crianças de todas a idades o contato com a modalidade de surf e o treino a longo prazo.

StartIUPI StartIUPI
Rua Febus Moniz, Nº19
Oeiras, 2780-234

Associação StartIUPI - Empreendedorismo e inspiração para crianças, jovens e adultos.

Escola de Futebol os Belenenses - Oeiras Escola de Futebol os Belenenses - Oeiras
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Oeiras, 2780-102

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APEE da Escola Secundária Luís de Freitas Branco APEE da Escola Secundária Luís de Freitas Branco
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Oeiras, 2774-516

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ABC do CCD - Centro de Estudo / Campos de Férias ABC do CCD - Centro de Estudo / Campos de Férias
Rua Embaixador Assis Chateaubriand, 65
Oeiras, 2780-198 OEIRAS

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Prova-Real Aconselhamento Escolar E Serviços Prova-Real Aconselhamento Escolar E Serviços
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Oeiras, 2770-232

Acima de tudo, somos uma equipa que adora trabalhar com crianças e jovens. São elas que nos movem

DJEM - For Djs & Producers DJEM - For Djs & Producers
Av.Edmundo Lima Bastos Loja N 3b
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