Open Chemistry

See the following -

First Open Chemistry Beta Release

Marcus Hanwell | Kitware Blog | April 11, 2013

We are pleased to announce the first beta release of the Open Chemistry suite of cross platform, open-source, BSD-licensed tools and libraries - Avogadro 2, MoleQueue and MongoChem. Read More »

Open Chemistry Project Raises Up the Next Generation of Researchers

In 2007 I took part in Google Summer of Code (GSoC) developing the Avogadro application. As we were developing Avogadro, we founded The Open Chemistry project as an umbrella project to develop related tools for chemistry and materials science. Our goal is to bring high quality open source tools to research communities working in these areas, and to develop other tools to complement the Avogadro molecular editor. This year we were very pleased to be selected as a mentoring organization for GSoC; a few of our mentors are Geoff Hutchison, Adam Tenderholt, David Koes, and Karol Langner, who are all long-time contributors in related projects. And, we were lucky to get three slots for student projects...

Open Chemistry Project Upholds Mission of Unorganization, The Blue Obelisk

Chemistry is not the most open field of scientific endeavor; in fact, as I began working more in the area (coming from a background in physics), I was surprised with the norms in the field. As a PhD student way back in 2003, I simply wanted to draw a 3D molecular structure on my operating system of choice (Linux), and be able to save an image for a paper/poster discussing my research. This proved to be nearly impossible, and in 2005 a group of like-minded researchers got together at a meeting of the American Chemical Society and formed an unorganization: The Blue Obelisk (named after their meeting place in San Diego)...

Open Chemistry, Semantic Physical Science and Kinecting Chemistry

Marcus Hanwell | Kitware Blog | February 10, 2012

Before the recent announcement of Open Chemistry, I was invited to the Semantic Physical Science Workshop and Symposium in Cambridge, England. The meeting was well attended, and Peter Murrary-Rust has put up videos of the talks given in the symposium on the final day. The meeting was ambitious, and we were able to get a lot done over a three day period.

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Open Source Dependency Management As A Balancing Act

During my career I have spent a lot of time packaging other people's code, writing my own, and working on large software frameworks. I have seen projects that still haven't released a stable version, never quite hitting 1.0, while others made 1.0 releases within months of beginning development, and then quickly moving on to 2.0, 3.0, etc. There is quite a variance in these release cycles, and this coupled with maintaining large projects can make things difficult. I will go through some of the decisions we have faced in projects I have worked on and the pressures on the project. On the one extreme, users would like to have a stable API that never changes, with dependencies that don't specify a minimum version so that they can choose whatever version works best...

Pistoia Alliance Launches New Chemical Safety Library Project

Press Release | Pistoia Alliance | November 10, 2015

The Pistoia Alliance...has started work on the Chemical Safety Library, a project which will allow for the capture and sharing of previously inaccessible reaction incident information to enhance laboratory safety...The Chemical Safety Library will see the creation of an informatics driven resource to allow all organizations to effectively share chemistry-related incident reports, delivering value from real life incidents and learnings. The data will be collected in a publicly available central resource and rule sets and triggers will be created that can be tied to scientists’ reaction planning tools, so that if an organization should attempt to repeat a procedure that previously resulted in an accident, a warning will be issued.

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Policy: NIH Plans to Enhance Reproducibility of Biomedical Research

In a recent editorial in the journal Nature, Francis Collins and Lawrence Tabak from the National Institutes of Health (NIH) discuss the concerns that NIH has with current lack of reproducibility in biomedical research, and propose steps for improving the repoducibility records. In their editorial they point out that we have traditionally considered science to be a self-correcting field. Given the expectation that over time, all reported works would be replicated by peers. Read More »

The Road to a Career in Open Source and Science

My journey from bench scientist to open science software developer and how I develop better tools for open, reproducible scientific research. Read More »