What is open science?
Open science is the movement to make scientific research (including publications, data, physical samples, and software) and its dissemination accessible to all levels of an inquiring society, amateur or professional.Open science is transparent and accessible knowledge that is shared and developed through collaborative networks.It encompasses practices such as publishing open research , campaigning for open access , encouraging scientists to practice open notebook science , and generally making it easier to publish and communicate scientific knowledge. (Source: Wikipedia, what else?)
Some useful links for beginners are listed on the openscience.com website …
Open science @ UNIGE and @UNIL
- Open Science @ UNIL: What is Open Access? How to’s! How to create your Orcid ID! Which journals allow post-print open acess deposit?
- Open Science @ UNIGE
- Open Science Services @ UNIL Medicine library
Open Source Neuroscience Training and (Data) Ressources
INCF Training Space
An online hub that aims to make neuroscience educational materials more accessible to the global neuroscience community developed in collaboration with INCF, HBP, SfN, FENS, IBRO, IEEE, BD2K, and iNeuro Initiative. As a hub, TS provides users with access to:
- Multimedia educational content from courses, conference lectures, and laboratory exercises from some of the world’s leading neuroscience institutes and societies
- Study tracks to facilitate self-guided study
- Tutorials on tools and open science resources for neuroscience research
- A Q&A forum
- A neuroscience encyclopedia that provides users with access to over 1.000.000 publicly available datasets as well as links to literature references and scientific abstracts
ReproNim: A Center for Reproducible Neuroimaging Computation
The ReproNim vision is to to help neuroimaging researchers to improve reproducibility of research findings:
- Find and Share data in a FAIR fashion (discover resources with NeuroBLAST)
- Comprehensively describe their data and analysis workflows in precisely replicable fashion (describe research processes with ReproIN and BrainVerse)
- Manage their computational resource options (do analyses with NICEMAN)
Innovations in Scholary Communication
hosts a great project listing a large number of tools and databases available for sharing research ideas and outcomes.
Courses, manuals and ressources suggested (and partially developed) by the Lemanic Neuroscience community
- (Open) Data Science
- Introductory course of statistical bayesian modeling (by Thierry Phenix, CHUV Lausanne)
- Basic Neuroimaging Data Science Course @ Foundation Campus Biotech Geneva
- An Introduction to Statistical Programming Methods with R – on online book (by Matthew Beckman, Stéphane Guerrier, Justin Lee, Roberto Molinari, Samuel Orso & Iegor Rudnytskyi)
- Collection of softwares developed by UNIGE, HUG, HES-SO
- NeuralEnsemble – a community-based initiative to promote and co-ordinate open-source software development in neuroscience . NeuralEnsemble hosts a number of software projects for computational and systems neuroscience, including PyNN , NeuroTools , Brian , Neo , OpenElectrophy , libNeuroML and Sumatra.
- Open Neuroscience – Repository for Open Source Neuroscience projects
- The repository of data analysis tools “Little Hitchiker’s guide to the brain ” by David Munoz Tord (UNIGE, now CHUV), as well as the “Data Wrangling Workshop ” he created.
- Inventory of the SIB-Swiss Bioinformatics training materials incl. Scripting and languages, Sequence data analysis, Computational methods and pipelines, Statistics and machine learning, Reproducibility and data management
- EEG / Neurophysiology
- Collection of interactive web applications for the visualisation, teaching and investigation of advanced scalp EEG and intracranial EEG analysis @Nicolas Roehri (UNIGE)
- STEN: Statistical Toolbox for Electrical Neuroimaging (by JF Knebel and M Notter, CHUV & UNIL)
- OpenEphys – open-source electrophysiology tools
- Reading materials of the EEGLAB workshop – a software for EEG processing
- Repository of the CHUV-DNC EEG platform – Power spectra and connectivity analyses on resting state EEG. Pipeline for reproducing results for comatose patients’ outcome prediction.
- Chronux : an open-source software package for the analysis of neural data. The tutorials were created for the 2006 SfN Dynamical Neuroscience workshop.
- MRI and Neurofeedback
- AFNI Bootcamp including theory/concepts of processing MRI data with AFNI, and showing hands-on usage of the graphical tools in the AFNI package.
- Matlab based tool to prepare for and coregister between OpenNFT Neurofeedback session(s) by Lucas Peek (UNIGE).
- hMRI-toolbox: A toolbox for quantitative MRI and in vivo histology using MRI (hMRI). The hMRI-toolbox is an easy-to-use open-source and flexible tool, for qMRI data handling and processing. It allows the estimation of high-quality multi-parameter qMRI maps (longitudinal and effective transverse relaxation rates R1 and R2*, proton density PD and magnetisation transfer MT saturation) (Weiskopf et al., 2013), followed by spatial registration in common space for statistical analysis (Draganski et al., 2011). Embedded in the Statistical Parametric Mapping (SPM) framework, it can be readily combined with existing SPM toolboxes for estimating diffusion MRI parameter maps, and it benefits from the extensive range of established SPM tools for high-accuracy spatial registration and statistical inferences.
Do not hesitate to join the platform LNDS Brain imaging students on Discord : A virtual space dedicated to mutual help, listening and sharing within the community of PhD students, post-docs and Msc students