Open Access across scales – from data to software, hardware and ideas
Event details
Date | 27.03.2019 |
Hour | 12:15 › 13:15 |
Speaker | Pavel Tomancak |
Location | |
Category | Conferences - Seminars |
The EPFL Open Science initiative invites you to this presentation by Pavel Tomancak, senior group leader at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, Germany.
ABSTRACT
Science is a collective endeavor and no matter what, we always stand on the shoulders of giants. Therefore, by definition, sharing everything scientific openly across the scientific community is paramount to progress. This obvious truth has been de-emphasized in the last decades of the 20th century as the scientific competition intensified. The Open Access (OA) movement emerged to partially remedy the situation. Pavel Tomancak will discuss his personal experiences with pushing OA agenda in various areas of scientific process including data, software, hardware, publications and institute operational models. Successes as well as failures will be highlighted, hopefully providing some inspiration for those who would like to try this at home.
The emphasis on open access in Pavel's career resulted in establishment of major resources such as Fiji and OpenSPIM.
Fiji (aka "Fiji Is Just ImageJ") is an open source image processing package based on ImageJ. Its main purpose is to provide a distribution of ImageJ with many bundled plugins. It was first presented to the ImageJ community in 2008. The original paper describing the core software project was published in 2012 and has now gathered over 12,000 citations.
OpenSPIM is an Open Access platform for applying and enhancing Selective Plane Illumination Microscopy (SPIM). As stated on their website, the researchers behind the initiative "hope that OpenSPIM in its radical openness will demonstrate that the benefits brought to science by the Open Source approach apply equally well to hardware." In particular, it is designed to be as accessible as possible:
- detailed, easy-to-follow build instructions
- off-the-shelf components and 3D-printed parts
- Modular and extensible design
- completely open blueprints
- completely Open Source
BIO
Pavel Tomancak studied Molecular Biology and Genetics at the Masaryk University in Brno, Czech Republic. He then did his PhD at the European Molecular Biology Laboratory in the field of Drosophila developmental genetics. During his post-doctoral time at the University of California in Berkeley at the laboratory of Gerald M. Rubin, he established image-based genome scale resources for patterns of gene expression in Drosophila embryos. Since 2005 he leads an independent research group at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden where he became senior research group leader in 2013. His laboratory continues to study patterns of gene expression during development by combining molecular, imaging and image analysis techniques. The group has lead a significant technological development aiming towards more complete quantitative description of gene expression patterns using light sheet microscopy. The Tomancak lab is expanding the systematic analysis of gene expression patterns to other Drosophila tissues and employing the comparative approach in other Drosophilids and invertebrate species.
Practical information
- Informed public
- Free
Organizer
- Luc Henry