Open source, open science Kitware, open-source platforms Jérôme Velut jerome.velut@kitware.com
Science 250 years ago, d Alembert (Discours préliminaire de l'encyclopédie, 1759) : reduction, systematic think Descartes, Hobbes, Hume : empirical method Newton : reproducible laws
Science Picture from xkcd.com «Science crisis»? Mobley, PLOS One, 2013 DOI: 10.1371/journal.pone.0063221 We found that ~50% of respondents had experienced at least one episode of the inability to reproduce published data
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
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
An open science platform
An open science platform
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)
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 2008 - $6.7 million DARPA contract 2010 EU, India offices established 2011 Awarded $24 million from DARPA (VIRAT, PerSEAS) 2011 - Tibbetts Award Winner (SBIR for IGSTK)
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
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.
The Visualization Toolkit (VTK) www.vtk.org 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: 4000+ users
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
ParaViewWeb http://paraviewweb.kitware.com
Medical Imaging ITK: www.itk.org Segmentation/Registration Image-Guided Surgery Simulation: haptic devices Clinical applications IGSTK, Slicer, CTK
Open-source Tools and Libraries Implementation of algorithms for dissemination Prototyping of new technologies Dissemination of research Modularization of applications
Scientific Data Management
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 www.kitware.com/midas
Scientific Data Management
Software Process Tools CMake/CTest/CDash (www.cmake.org) Easily configure projects on different platforms Started in 2000 with ITK CMake downloads: +3000/day CDash: 300 public projects
Software Process
CDash Dashboard www.cdash.org
Jérôme Velut, Kitware jerome.velut@kitware.com