Open Science Workshops 2015

EPFL Library is pleased to invite you to the:





The goal of these events is to promote Open Science, Open Access and Open Data movements and support their sustainability. The workshops will take place on November 3rd, 12th, 17th and 26th 2015, from 5.30pm to 7.30pm at the EPFL Campus (Switzerland).

During the workshops, participants will discuss about Open Science evolutions, challenges and stakes. Partakers are encouraged to share their experience and to foster interactive exchanges. After a short theoretical introduction, participants will experiment software/applications through practical exercises.

The event targets all those who would like to learn more about Open Science, including representatives of local politics, academic communities (researchers, doctoral students, professors, administrators), as well as publishing or information professionals, and IT support officers.


General programme

Tuesday 3 November                  Reproducible Research using IPython, by Amir Hesam Salavati and Robin Scheibler, 5.30pm – 7.30pm, BC 02.
Thursday 12 November Open Access Publication: the Good, the Bad and the Ugly, by the EPFL Library team,
Tuesday 17 November DMPOnline, by Sarah Jones, 5.30pm – 7.30pm, BC 02.
Thursday 26 November Data/Text mining, by Renaud Richardet, 5.30pm – 7.30pm, BC 02



Workshop 1 Reproducible Research using IPython interactive publications
Date and Room Tuesday 3rd November, 5.30pm-7.30pm, BC 02
Abstract               A large part of modern research is increasingly supported by sophisticated computer run algorithms.  As such, these algorithms have become an integral part of the information needed to reproduce scientific results in all fields. Even when the publication is accompanied by data, it is not enough if the algorithms to make sense of it are not available. Luckily, tools that can help researchers to make their computational results reproducible are available.  IPython is such a tool. It relies on Python, a robust open source and general purpose programming language. IPython comes with IPython notebooks, a unique tool that is very well suited for sharing the results of computational research. It also allows users to perform interactive
computing as well as exporting the notebook to a variety of other document formats. During this workshop, we will demonstrate how this tool can support research by drawing examples from various fields. A short introduction will be followed by an extensive hands-on session.
Logistical information People bring their own laptop and we send them instructions to install ipython in advance, that way your machine will be ready for future use / We keep 5 minutes times at the beginning of the workshop devoted to help people that had trouble with the installation / The library can provide laptops during the workshop. INSTRUCTIONS AND PROCEDURE BEFORE THE WORKSHOP.
Speakers Amir Hesam Salavati and Robin Scheibler
Biographies Hesam Salavati received his B.Sc. and M.Sc. in Communication Systems and Science from Sharif University of Technology, Iran in 2006 and 2008. In 2014, he received his Ph.D in Computer and Communication Sciences school of École Polytechnique Fédérale de Lausanne (EPFL). He is with the laboratory Audiovisual Communications (LCAV) at EPFL where he is in charge of activities related to reproducible research at LCAV. His research interests include neural signal processing, coding algorithms, and web design. Robin Scheibler received the B.Sc. and M.Sc. in Communications Systems from École Polytechnique Fédérale de Lausanne (EPFL), Switzerland in 2006 and 2009, respectively. From 2009 to 2010, he was with IBM Research – Zürich. After this, he was with the NEC Media Information Processing group in Kawasaki, Japan from 2011 to 2012. He then returned to EPFL where he is working towards the Ph.D. degree at the Laboratory for Audiovisual Communications. His research interests lie in algorithmic signal processing, speech processing, and acoustic beamforming.
Online presentation General introduction by Amir Hesam
How to use GitHub? by Robin Scheibler
All the presentation supports



Workshop 2 Open Access Publication: the Good, the Bad and the Ugly                                                  
Date and Room Thursday 12th November, 5.30pm-7.30pm, BC 02
Abstract               The landscape of academic publishing has greatly evolved over the last decades. With the emergence of Open Access, the journal subscription-based traditional model in which authors grant publishers with exclusive rights on their works, is no longer the standard. Authors are now facing a plethora publishing models and must find the best trade-off in order to both ensure the optimal diffusion of their results and meet the funders’ requirements. During this workshop, we will follow the journey of an academic publication while focusing on how you can get the most benefits from Open Access and data publication. We will explore and discuss such issues and challenges as how to preserve your author’s rights, how to find the best journals and avoid legal pitfalls, how to understand and meet the funders’ requirements regarding the deposit of your paper as well as the dissemination of your research data.
Level Beginner
Speakers The EPFL Library team
Biographies Aude Dieudé received her PhD from Duke University and specializes in research data management at the École Polytechnique Fédérale de Lausanne (EPFL). She coordinates the data management plan support service at the EPFL and offers training on how to optimize research data management. In addition, she is involved in a Swiss national project (DLCM) focusing on providing sustainable and tangible solutions at a national level to implement research data life-cycle management.

Jan Krause works at the EPFL Library. He is involved in the research data management support service as well as in the national Data Lifecycle Management (DLCM) project. Jan has been trained as a scientist and has worked in a wetlab, an High Performance Computing group, on bibliographic similarity analysis. Previously, he was a system librarian at CERN, the University of Geneva and CHUV. His main focuses are on (meta)data standards and data sharing and archiving technologies.

Béatrice Marselli received her B.Sc. and M.Sc. in Chemistry from University of Geneva, and her Ph.D. in Chemical Engineering from Ecole Polytechnique Fédérale de Lausanne (EPFL). She became editorial assistant for two academic journals from the American Chemical Society: Inorganic Chemistry at Stanford University for four years and Biomacromolecules for six years at EPFL. She joined the EPFL Library in October 2014 to work on Open Access and as liaison librarian for Materials Science and Microengineering Institutes.

Julien Junod works since 2010 at the EPFL library and is the liaison librarian for mathematics.

Online presentation Open Access Publication: the Good, the Bad and the Ugly (PDF) 



Workshop 3 DMPonline workshop
Date and Room Tuesday 17th November, 5.30pm-7.30pm, BC 02
Abstract               A workshop to introduce researchers to the concept of data management planning and benefits of writing a DMP. The Digital Curation Centre’s DMPonline tool will be demonstrated and used in an exercise on writing plans. Useful resources and examples will also be shared to takeaway.      
Level Beginner
Speaker Sarah Jones, Senior Institutional Support Officer
Biographies Sarah Jones works at the Digital Curation Center, a UK national service to support the higher education sector with research data management. She coordinates work on DMPonline and undertakes research on data policy and data management planning. She is also involved in the EC-funded FOSTER and EUDAT projects, fostering open science by training researchers and providing services for open access et open data.
Online presentation DMPonline (PDF)



Workshop 4 Data/Text Mining                                                                                                                           
Date and Room Thursday 26th November, 5.30pm-7.30pm, BC 02
Abstract               A practical workshop to introduce researchers to data and text mining. In many scientific domains, the primary form of knowledge dissemination is through published articles. One challenge for researchers is finding methods to make the knowledge from the tremendous backlog of publications accessible for search and analysis. In this workshop, we will review various text mining methods and walk through the various steps of data acquisition, data processing and data presentation. All steps are illustrated with practical examples in Python. In the last part of the workshop, each participant will have the opportunity to present a text-mining project that is relevant to her/his work. We will then briefly discuss together potential strategies and solutions.

1) Introduction
2) Basics
   a) quick start with UNIX tools
   b) regular expressions
   c) know your text editor
3) Data acquisition
   a) strategy, considerations, copyrights
   b) crawling data from an API (PubMed)
   c) scraping data from a website
4) Data processing
   a) parsing, selecting and transforming data with Pandas
   b) extracting text from pdfs
   c) text processing with NLTK
   d) full-text search with Elasticsearch
5) Data presentation
    a) a simple website to present data & gather user feedback
    b) data presentation frameworks
6) Your usecases

Each participant will take 5 min (alone or in small groups) to present a text-mining project that is relevant to her/his work. We will then briefly discuss together potential strategies and solutions.

Level Beginner
Speakers Renaud Richardet, PhD candidate, EPFL.
Biography Renaud Richardet received his PhD from EPFL’s Blue Brain project and works on large scale natural language processing applications for the biomedical domain.
Prior to joining EPFL, Renaud held various positions as research scientist and senior developer in Switzerland, India and in the USA. His primary fields of interests are natural language processing (NLP), deep learning, big data, and open source software.
All the documents



We are looking forward to meeting you on November 3rd, 12th, 17th and 26th 2015!

EPFL Library Team