Open source, open science
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1 Open source, open science Kitware, open-source platforms Jérôme Velut
2 Science 250 years ago, d Alembert (Discours préliminaire de l'encyclopédie, 1759) : reduction, systematic think Descartes, Hobbes, Hume : empirical method Newton : reproducible laws
3 Science Picture from xkcd.com «Science crisis»? Mobley, PLOS One, 2013 DOI: /journal.pone We found that ~50% of respondents had experienced at least one episode of the inability to reproduce published data
4 Open science Challenges : Increasing amount of knowledge Increasing amount of data Fundings? Communicate Creative commons Open access Open science Collaborate Wikis Git Reproduce Open source tools
5 An open science platform Example 1 - Insight Journal Communicate (paper publishing) Collaborate (open source code) Reproduce (open source code, review management) Example 2 - MICCAI challenge Medical imaging challenge Training set of images Automatic processing of testing images
6 An open science platform
7 An open science platform
8 Kitware History Founded in 1998 Support VTK (Visualization Toolkit) software Five founders from GE Research Now ~120 employees 75+ PhD and Masters Research-quality staff $20 million revenue Privately owned No debt Offices Clifton Park, NY (USA) Chapel Hill, NC (USA) Santa Fe, NM (USA) Lyon (France)
9 Company Background 1998 Formed to support VTK software 1999 Contracted to develop ITK image analysis software by NLM 2000 Collaborative agreement (with Los Alamos, Sandia) to develop ParaView 2004 NIH NAMIC Award (National Center of Biomedical Computation) 2006 Informatics development (Titan) initiated with Sandia National Labs 2006 Chapel Hill office established 2007 Computer Vision group established $6.7 million DARPA contract 2010 EU, India offices established 2011 Awarded $24 million from DARPA (VIRAT, PerSEAS) Tibbetts Award Winner (SBIR for IGSTK)
10
11 Business Model Open source software Services and support Consulting Collaborative R&D Commercial products Value-added products Applications built on high quality, open source base Custom (proprietary) software frameworks
12 Open Source Systems VTK Visualization Toolkit ParaView Large data visualization Titan Informatics Toolkit ITK Insight image analysis toolkit 3D Slicer Medical research platform CMake Cross-Platform Build IGSTK, CTK, VXL, Avogadro, more.
13 The Visualization Toolkit (VTK) Started in 1993 at GE Visualization Library Written in C++ (+5.5 million LOC) Automatic binding for Java, TCL, Python Portable by design: Linux, Windows, Mac OSX, Solaris Very active community: users
14 ParaView OpenSource (BSD) Based on VTK C++/Qt Python support Very active community (HPC wire award) Multi-core support (MPI) Co-Processing (in-situ) More than 50 news readers Visit plugins are supported User s guide online 1 billion cell asteroid detonation simulation
15 ParaViewWeb
16 Medical Imaging ITK: Segmentation/Registration Image-Guided Surgery Simulation: haptic devices Clinical applications IGSTK, Slicer, CTK
17 Open-source Tools and Libraries Implementation of algorithms for dissemination Prototyping of new technologies Dissemination of research Modularization of applications
18 Scientific Data Management
19 MIDAS Web-based digital archiving system Archive, search and manage (any) digital media Open Source (BSD) Started in 2005, based on DSpace Flexible and modular Framework External API to manage and access data: REST, C++ Grid computing Online visualization and interaction
20 Scientific Data Management
21 Software Process Tools CMake/CTest/CDash ( Easily configure projects on different platforms Started in 2000 with ITK CMake downloads: +3000/day CDash: 300 public projects
22 Software Process
23 CDash Dashboard
24 Jérôme Velut, Kitware
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