Open Science, Open Access and Open Source

abernard102@gmail.com 2012-05-01

Summary:

... “As a PhD student I enjoyed learning more about materials, and was excited to be working with gold nanoparticles and research into how we might make real devices out of this novel new material in the Nanomaterial Engineering Group. It was exciting, challenging and fascinating using techniques such as X-ray and neutron reflectometry, electron and atomic force microscopy and Langmuir-Blodgett troughs. As I learned more through my work I became frustrated with the quality of the software I used, and had always imagined that "real scientists" had better tools available to them. It became even more frustrating when I realized how bad some of the instrument control software was, and how so many of the file formats could only be used in one or two expensive and hard to use programs that only worked on one or two platforms. Towards the end of my PhD I decided I would like to take some action. I had been trying to draw and render images of molecular structures, and wanted a way to do simple geometry optimizations for posters, papers and web pages... As I searched for a better way I came across some open source libraries and tools. I found a program run by Google called ‘Summer of Code’ where they offered me the opportunity to "flip bits not burgers". I was extremely lucky to find an idea on KDE's idea page for a molecule editor in Kalzium. I was very excited, and had been using KDE for many years. This was a pivotal moment for me, where my life and career took a twist I never expected into the world of open science - and I have loved every minute of it. It was through that work that I became involved in the Avogadro project, and later Open Babel and met Geoff who later that year offered me a position inhis new research group. This was an exciting opportunity as not only did we share a passion for correlating experimental and computational techniques, Geoff was also very active in open chemistry. After I moved out to Pittsburgh Geoff introduced me to the Blue Obelisk, and I now proudly count myself as one of their un-members. We published an open access paper on the Blue Obelisk five years on last year... I met Bill Hoffman from Kitware. I knew that Kitware developed CMake, but beyond that was not really aware of what they did. It turned out that they were involved in much more than just CMake, with open source tools and frameworks such as VTK, ParaView, ITK,CDash and more. They had been working on open scientific software for over a decade, and they were hiring! ... After accepting a position with Kitware in 2009 one thing I never really appreciated was just how poor access is to publicly funded research. I can no longer access scientific papers I and others wrote, that were funded with tax payer money from both the UK and the US! I think that is terrible, and later realized I had become part of the scholarly poor... There is currently raging debate on open access, and campaigns such as The Cost of Knowledge need our support. The products of publicly funded research should be available to all, whether they are in academia, industry, government or anywhere else. There are too many black boxes in science today, too much published work that is not available to all or reproduced by others. Mathematics used to be the language of science, but more and more it is computer software that is needed to learn more, and too much of this code is closed, unpublished and poorly shared. Papers must include mathematical proofs, or refer to proofs already published, but it is common to see work published that used closed, proprietary package X to conduct a simulation. This is changing, and Scientific American recently published an article on how "Secret Computer Code Threatens Science". Science also published an article about "Shining Light into Black Boxes", detailing the growing problem of witheld source code preventing meaningful peer review and reproducibility of research. Michael Nielsen published a book called "Reinventing Discovery" that talks about the value of networked science, and is well worth a read if you have not yet had a chance. The Panton Principles outline the need to make scientific data open, and the Science Code Manifesto calls for openly available code in science. The core goals of the Blue Obelisk are open data, open standards and open source. I think for science to progress we must embrace openness, and sharing and resist the urge to hoard data building up small empires on proprietary code and data. One thing I hope to see come from all of the controversy of the Research Works Act is a clarification that publicly funded research should be available to all, whether you think they will understand it or not. Scientists need to get better at communicating with the general public, and being more transparent about how research is done. I think open science will give us a chance to increase public engagement in science, which seems to be a growing problem in an age where we can all access the internet and a wealth of knowledge available on it. I think that we need to figure out sustainable ways to fund the development of open

Link:

http://blog.cryos.org/archives/258-Open-Science,-Open-Access-and-Open-Source.html

Updated:

08/16/2012, 06:08

From feeds:

Open Access Tracking Project (OATP) » abernard102@gmail.com

Tags:

oa.new oa.data oa.policies oa.licensing oa.comment oa.usa oa.legislation oa.rwa oa.nih oa.advocacy oa.signatures oa.petitions oa.boycotts oa.copyright oa.panton oa.open_science oa.declarations oa.crowd oa.oer oa.funding oa.tools oa.sustainability oa.chemistry oa.floss oa.engineering oa.kde oa.science_code_manifesto oa.cdash oa.itk oa.paraview oa.cmake oa.vtk oa.kitware oa.blue_obelisk oa.open_babel oa.avogadro oa.kalzium oa.nano oa.libre oa.economics_of

Authors:

abernard

Date tagged:

05/01/2012, 09:38

Date published:

04/23/2012, 12:53