- Posts tagged openscience
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HPCwire: Computational Chemistry Package NWChem Goes Open Source
NWChem, the premier computational chemistry package developed at the Department of Energy's EMSL, is going open source -- allowing computer scientists worldwide to contribute to its future development and opening its use to more researchers and students.
Good news.
SarahAskew » Solo10: Online vs. Offline
Science writer Ed Yong recently wrote about the difference between writing for writing, and writing for change. One thing to remember is that there is no such thing as “blogging”. Blogging describes a medium, not a goal. It covers a whole spectrum of styles and purposes, and “success criteria” are therefore just as diverse. To have debates about the point of “science blogging” may not be a very useful exercise.
I'm not a science blogger, although I am a scientist who has a nominal blog. Later in the article, Sarah makes the statement, "I think long as you’re clear about what it is you’re trying to achieve, whatever the scale, and make an effort to find out how you’re doing (this step is often missing), you’re inherently on the right track." I think she's right on the money.
One of the projects I am involved with has a blog, which has largely lain fallow for some time (but hopefully not in the future!). But, I think it could be the mechanism for engaging community interest -- especially to raise the level of "external" participation. (Although, we live in an Open Source world -- "external" is losing its meaning.) But, while I think this probably will work for yt, I'm skeptical the same type of approach would work for the actual simulation code, simply because the type of participation the two communities foster is different.
Free Software Needs Free Tools :: Benjamin Mako Hill
Over the last decade, free software developers have been repeatedly tempted by development tools that offer the ability to build free software more efficiently or powerfully.
The only cost, we are told, is that the tools themselves are nonfree or run as network services with code we cannot see, copy, or run ourselves. In their decisions to use these tools and services -- services such as BitKeeper, SourceForge, Google Code and GitHub -- free software developers have made "ends-justify-the-means" decisions that trade away the freedom of both their developer communities and their users. These decisions to embrace nonfree and private development tools undermine our credibility in advocating for software freedom and compromise our freedom, and that of our users, in ways that we should reject.
This is a good point, and one that I think deserves some scrutiny. The open source KForge project provides an opportunity to escape hosts like SourceForge, Google Code, GitHub and Bitbucket, but it is relatively difficult to deploy on commodity hosting. (This week I had the opportunity to talk to someone who had deployed it.) I'm guilty of storing many of my scientific projects on Google Code and Bitbucket, but one of my main projects is hosted privately on a server I pay for, using only Free Software.
One of the issues I see with scientific programming endeavors is that often the self-hosting option presents some red tape, whereas the hosted option is much simpler and easier -- particularly if the project itself is cross-institutional. This is one of the reasons I pushed for our primary simulation platform to be hosted at Google Code, rather than on a local, university-hosted server.
Dear researcher, which side of history will you be on? | Mendeley Blog
We came to the conclusion that technology is finally at a point that if we don’t use it now, then we are holding back the progress of science. And what exactly are we to use technology on? Open science/data/access.
Revisiting Ethos | jonobacon@home
When I first heard about Free Software in 1998 I was mesmerized by it’s potential. Sure, back then the software was complex and some would argue ugly, but underneath the rough edges was a thing of beauty — the opportunity for people to come together to make new things, and anyone with the inclination and energy could take part.
Jono's description really rings home for me. When I first really started hearing about FLOSS, I was 18. I'd been using Linux and Unix for seven years (but only on dial-in BBSes and the like) but I'd never considered using it on my desktop. And then I picked up a copy of SUSE 6.1, installed it, and started looking beneath the surface. I still believe in the principles, but it's hard not to get frustrated with where computing is going. I've tried to use those principles in my research, pushing my code and my data into the open while encouraging my colleagues and collaborators to do so as well. We've been successful so far, but the Grand Experiment (as my current mentor likes to call it) is just beginning. (More on that as it occurs.) In many ways the FLOSS community and the Scientific communities are very similar, but the cross-talk is sadly limited.
To answer the prompt from Jono that I didn't quote above, I'm passionate about Free Software and Open Source software because I want my kids to have the same opportunities and the same encouragements that I did. And because I think it's really guided me, my personal and my professional interactions in many ways, and I want to make sure that spirit of collaboration, of openness, of tinkering and problem solving never dies out.
Michael Nielsen » Cameron Neylon on practical steps toward open science
The most critical issue however is rapid deployment of expertise to specific problems. To apply a distributed rapid innovation model we need the means to rapidly identify the very limited number of people with appropriate expertise to solve the problem at hand. We also need to rethink our research processes to make them more modular so that they can be divided up and distributed. Finally we need capacity in the system that makes it possible for expertise to actually be rapidly deployed. Its not clear to me how we achieve these goals although things like Innocentive, CoLab, Friendfeed, and others are pointing out potential directions. We are a long way from delivering on the promise and its not clear what a practical route there is.
Practical steps: more effective communication mechanisms will be driven by rewarding people for re-use of their work. Capacity can be added by baseline funding. Modularity is an attitude and a design approach which we will probably need to build into training and will be hard to do in a community where everything is bespoke and great pride is taken in eating our own dogfood but never trusting anyone else’s…
I find this particularly compelling, especially in light of some of the growing pains yt has been having. We're trying to build something that's useful, without losing sight of our own personal goals, and it's difficult at times. But we've been having some amazing successes, and I think it's worth it.
Four Big Ideas from the Open Science Summit 2010
Our new vision for CoLab is to enable scientific debate around any piece of scientific content. We want to make it stupid easy to center a discussion around protocols, data, plots, published papers, papers in progress, simulations, code, or any other component of scientific research. As an experimentalist, I should be able to import a lab protocol, raw data, or manipulable plots based on a live feed from that raw data and discuss it online with collaborators across the globe. As a computational scientist, I should be able to import code or live simulations and troubleshoot online with anyone in the world who might be able to help. As a member of a journal club, I should be able to import a published paper and collaboratively highlight and annotate in-line with colleagues, from those in the lab next door to those in another country. As a researcher ready to publish, I should be able to host a working version of my paper online, collaboratively edit with any of my colleagues, and submit a link directly to a journal, without being forced to download the paper and make finishing touches offline. In short, as a scientist, I should be able to easily and openly discuss any piece of my science with my entire scientific community.
Interesting vision. CoLab is something to keep a close eye on.
