Open Software Initiative (OSI) day

lundi 26 oct. 2015, 08:30 → 17:30 Europe/Paris

Alexandre Gramfort (Telecom ParisTech, CNRS), Balázs Kégl (LAL)

Day dedicated to data science tools and engineering efforts at CDS, with presentations from funded projects, students, and invited speakers.

The event will take place in the main Auditorium of the Linear Accelerator Laboratory (LAL), building 200 on the UPSud Orsay campus. Information on getting to LAL is available here.

Webcast of the event here.

Current program:
https://docs.google.com/document/d/1W_4VOXuXg15YJTMZC7ax20SMpbBJALdh0HZA1foZIEA/edit?usp=sharing

Come back home.

1 Welcome participants & coffee¶

2 Introduction¶

Orateur: Alexandre Gramfort (Telecom ParisTech, CNRS)

Transparents slides_CDS_OSI_day.pdf

Video http://webcast.in2p3.fr/videos-introduction_osi_day

Session 1¶

3 Keynote Speech 1: Jupyter at BIDS: building the tools and the institutions for data science¶

In this talk, I will discuss both the architecture and recent developments in the Jupyter project, (the multi-language platform evolved from the IPython system for interactive Python). Jupyter is a project aimed at a broad class of problems in data science, and at UC Berkeley, its development today takes place in a new kind of institutional context: the Berkeley Institute for Data Science (BIDS). I will also discuss the genesis of BIDS, and how this interdisciplinary space tries to foster a culture of collaboration, open research, and where specifically, the development of open source software for scientific research is a first-class citizen.

Orateur: Fernando Perez (UC Berkeley - original author of IPython and driver of Project Jupiter)

Slides jupyter-bids-paris-oct-2015-fperez_(1).pdf

Video http://webcast.in2p3.fr/videos-keynote_speech__jupyter_at_bids_building_the_tools_and_the_institutions_for_data_science

4 Sphinx-Gallery, Package documentation made easy¶

Orateur: Oscar Nájera (U. Paris-Sud/LPS)

Slides osi_talk_Oscar.zip

Video http://webcast.in2p3.fr/videos-sphinxgallery_package_documentation_made_easy

10:30 Coffee Break

5 Py-Earth, Multivariate Adaptive Regression Splines in Python¶

Orateur: Mehdi Cherti (CNRS/LAL, AppStat)

Slides mehdi-cherti-py-earth.pdf

Video http://webcast.in2p3.fr/videos-pyearth_multivariate_adaptive_regression_splines_in_python

6 MNE from shell scripts and Unix commands to Python¶

Orateur: Lorenzo de Santis

Slides OSI_presentation_desantis.pdf

Video http://webcast.in2p3.fr/videos-mne_from_shell_scripts_and_unix_commands_to_python

7 Reproducible research in Bioinformatics: Scientific Workflows, provenance and beyond¶

Orateur: Sarah Cohen-Boulakia (U. Paris-Sud/LRI)

Slides dataCenterSaclay.pdf

Video http://webcast.in2p3.fr/videos-reproducible_research_in_bioinformatics_scientifique_workflows_provenance_and_beyond

8 LoOPS Network for developers at Paris-Saclay¶

LoOPS is a network of scientific software developers in Higher Education and Research Institutions in the southwest of Paris. The mission of the network is to facilitate the sharing of practices, expertise and knowledge among developers in order to allow everyone to progress in its software development activity.

Orateur: Karin Dassas (CNRS/IDOC)

Slides Karin.pdf

Video http://webcast.in2p3.fr/videos-loops_network_for_developers_at_parissaclay

9 The io.datascience DaaS platform¶

Orateur: Mme Karima Rafes (LRI)

Video http://webcast.in2p3.fr/videos-the_iodatascience_daas_platform

12:30 Lunch Break

Session 2¶

10 Building a service-oriented platform for online physiological data analysis.¶

Nowadays it is possible to online collect, classify, and process data with the proper software platforms. Along with advances in signal processing and "big data" algorithms we can use them as research facilities or even as automatic diagnostic tools. Specifically, we are building such a platform applied to physiological signals. It involves a large group of researchers in mathematics, software engineers, and neurologists in the framework of the COGNAC-C project.

Orateur: Miguel Colom (ENS-Cachan/CMLA)

Slides presentation.pdf

Video http://webcast.in2p3.fr/videos-building_a_serviceoriented_platform_for_online_physiological_data_analysis

11 Automation for chemical data analysis techniques¶

Chemical data acquired from different analytical techniques and disparate analytics platforms has become high volume and lacks of well organized. The raw data is formed under several different proprietary formats. All data requires to convert to a common open data formats for storage, analysis, pre-treatment and treatment. The current scientific workflows are manually done and requires a certain knowledge of programming languages. We propose a solution which can technologize the scientific workflow. Furthermore, the system enables to automate workflows with less efforts and without having manually initiate the complex configuration.

Orateur: Diem Bui Thi

Slides diembui.pptx.pptx

Video http://webcast.in2p3.fr/videos-automation_for_chemical_data_analysis_techniques

12 Information Extraction Challenge for Gene Regulation Network in plant¶

Orateur: Estelle Chaix (INRA/MIG)

Slides OSI_Chaix_Estelle.pdf

Video http://webcast.in2p3.fr/videos-information_extraction_challenge_for_gene_regulation_network_in_plant

15:00 Coffee Break

13 Mining brain imaging data: lessons learned from nilearn and joblib¶

This talk will present useful patterns and lessons learned for efficient application of machine learning to data too big to fit in memory, in the context of brain imaging applications. The focus here is sharing insights gained while using and developing nilearn and joblib, as many of the lessons are not specific to brain imaging.

Orateur: Loïc Estève (INRIA)

Slides 2015_cds_nilearn_joblib.pdf

Video http://webcast.in2p3.fr/videos-mining_brain_imaging_data_lessons_learned_from_nilearn_and_joblib

14 A customizable framework for neurophysiology data management and provenance tracking¶

Orateur: Jonathan Duperrier (CNRS)

Slides helmholtz_duperrier_OSI_2015.pdf

Video http://webcast.in2p3.fr/videos-a_customizable_framework_for_neurophysiology_data_management_and_provenance_tracking

15 Anomaly detection algorithms in Scikit-Learn¶

Orateur: Nicolas Goix (Telecom Paristech)

Slides nicolas_goix_osi_presentation.pdf

Video http://webcast.in2p3.fr/videos-anomaly_detection_algorithms_in_scikitlearn

16 Structured Prediction with Opera-Lib¶

Orateur: Romain Brault (CNRS/IBISC)

Slides Romain_Brault_CDS.pdf

Video http://webcast.in2p3.fr/videos-structured_prediction_with_operalib

17 Keynote Speech 2: Software and engineering efforts at NYU Center for Datascience¶

Orateur: Andreas Mueller (NYU)

Slides nyu_cds_engineering_osi_day_Saclay_2015-expanded.pdf

Video http://webcast.in2p3.fr/videos-keynote_speech__software_and_engineering_efforts_at_nyu_center_for_datascience