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Author Archives: Dan Gezelter
On Reproducibility
I just got back from a fascinating one-day workshop on “Data and Code Sharing in Computational Sciences” that was organized by Victoria Stodden of the Yale Internet Society Project. The workshop had a wide-ranging collection of contributors including representatives of … Continue reading
Posted in Conferences, Open Data, open science, Policy, Science
3 Comments
Sad news about Warren DeLano
I just heard the sad news about Warren DeLano, one of the giants of open source scientific software (and the author of PyMOL). Warren passed away suddenly a few days ago. Like everyone else, I’m stunned and saddened by this … Continue reading
Posted in open science, Science, Software
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Debellor
Debellor is an open source Java framework for scalable data mining and machine learning. You may implement your own algorithms in Debellor’s architecture and combine them with pre-existing ones to create complex data processing networks and experimental setups. The unique … Continue reading
Science Laboratory Inventory
Science Laboratory Inventory Control Management System and Orders: Web-based system that is useful for managing chemical and equipment inventory management and handling science labs orders from teachers to technicians for their practical sessions. Find Science Laboratory Inventory at: http://sciencelabinv.sourceforge.net
Posted in Tools
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Webolab
A web-based platform for collaborative research and high-performance computing interface, a tool for implementation of virtual labs. Supports Condor cluster management engine. Find Webolab at: http://www.webolab.net
Posted in Tools
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OpenOpt
Universal cross-platform (Win, Linux, Mac OS) Python-written numerical optimization toolbox. License: new BSD. Problems: NLP, LP, QP, SDP, SOCP, DFP(Non-linear Data Fit), NSP(nonsmooth), MILP, LSP, LLSP, MMP, GLP, MINLP etc. Connects to dozens of solvers (some are C- or Fortran-written). … Continue reading
Posted in Optimization
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What, exactly, is Open Science?
I was recently asked to define what Open Science means. It would have been relatively easy to fall back on a litany of “Open Source, Open Data, Open Access, Open Notebook”, but these are just shorthand for four fundamental goals: … Continue reading
Posted in Open Data, open science, Policy, Science
56 Comments
Adevs
Adevs (A Discrete EVent System simulator) is a C++ library for constructing discrete event simulations based on the Parallel DEVS and Dynamic DEVS (dynDEVS) formalisms. Find Adevs at: http://www.ornl.gov/~1qn/adevs
Posted in Simulation and Modeling
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Saros: Distributed Pair Programming
I’m a big fan of pair programming, which is one of the primary modes of software development in my research group. Usually, two people sitting together can spot errors that one alone can’t, and the pace of the coding and … Continue reading
Saros
Saros is a research project to enable distributed pair programming (also called remote pair programming) in the Java IDE Eclipse. Saros supports real-time collaboration by two and more peers and adds many features to increase awareness and presence regarding the … Continue reading
Posted in Software Engineering, Tools
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