OpenScience / Science



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

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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

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Posted in Open Data, open science, Policy, Science | 53 Comments

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

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Posted in Science, Software | 1 Comment

Scientific Software Wants To Be Free

Go read this wonderful manifesto over at arXiv: Astronomical Software Wants To Be Free: A Manifesto by Weiner et al. The authors talk about some of the barriers to astronimical software development that are true in all scientific fields. The … Continue reading

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Posted in open science, Policy, Science | 4 Comments

Quantum Espresso!

I just got email from Brandon Wood about an open source project called Quantum Espresso (formerly known as PWSCF), which is a rather extensive open-source project for DFT-based electronic structure calculations. It appears to be a refactoring of some established … Continue reading

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Posted in open science, Science, Software | 5 Comments

New Software: Reference Tools, Atomic Physics, and Engineering

Some new software to point out today: In the Tools section, we have a new link to cb2bib a tool for rapidly extracting unformatted bibliographic references from email alerts, journal web pages, and PDF files. In the Atomic & Molecular … Continue reading

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Earmarks for Science

At the debate last night, John McCain brought up (twice!) for special scorn an example of spending on earmarks. His target? The “overhead projector for a planetarium”. It wasn’t the first time he’s brought up this earmark request up either. … Continue reading

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Posted in Policy, Science | 2 Comments

New Software: Data Mining

Some new software is in our Knowledge Discovery and Data Mining section. I can remember a time when “data mining” was a bit of an epithet in science (like “fishing expedition”), but now it has become an established way of … Continue reading

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Posted in Science, Software | Tagged | 6 Comments

Researching Open Science

I don’t know how I missed this before, but there’s a really interesting article from 2006 up at the Harvard Business School “Working Knowledge” site. It details some of Karim Lakhani‘s results from a paper called ‘The Value of Openness … Continue reading

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Posted in open science, Science | Tagged , | 1 Comment

Automated out-of-plane finder?

The code I’ve been working on has some cool features. If you give it a list of atoms and bonds, it automatically figures out bend and dihedral interactions using simple graph concepts. That is, if the molecule has a bond … Continue reading

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