Hi, As we push into 2013, and development of the Avogadro 2 code base is progressing I wanted to talk a little about what we are up to. Please bear in mind that development is still at a very alpha level, but under the open source mantra of "release early, release often", I wanted to share. We attended the ACS meeting in Philadelphia last year and presented a poster summarizing some aspects of the work,
http://www.slideshare.net/cryos/open-chemistry-realizing-open-data-open-standards-and-open-source There are also some slides from a talk I gave discussing Avogadro and the wider Open Chemistry project, http://www.slideshare.net/cryos/avogadro-open-chemistry-and-semantics If you would like to know more about Open Chemistry, and how it relates to Avogadro development an article I wrote for the Source (a little old now, but still relevant), http://kitware.com/source/home/post/39 The core of development is taking place in the AvogadroLibs repository, where several libraries are being developed to focus on developing a scalable chemical editor and analysis framework. Integration (optional) with related applications for desktop HPC integration (MoleQueue) and cheminformatics (MongoChem) offer a fuller solution, but Avogadro will remain usable on its own. We have been developing a communication protocol that leverages JSON RPC 2 and local sockets to facilitate communication between the applications, if the named socket does not exist the functionality can be disabled at runtime, and this means that direct linking is not required between the components. Much of our development effort over the past year has focused on desktop HPC integration, core library functionality, databases and informatics. In the last few months we have had more time to devote to Avogadro development, and we will be pushing hard during January to develop out the core application functionality. We have been using this as an opportunity to examine what we did well in Avogadro 1, while rewriting pieces that were not optimal. What you see in the repository is the rewritten core, with only a few of the classes ported at present. http://packages.kitware.com/community/5 https://github.com/OpenChemistry The Avogadro 2 libraries are licensed using the BSD 3-clause license, pieces that cannot be relicensed will have to be rewritten. One large departure from Avogadro 1.x is that Open Babel cannot be used/linked to as it is GPLv2 only, but we can still call the command line components in a separate process and we will add that functionality soon so that we can maintain support for the large number of file formats, and reuse other functionality as it makes sense. We will focus on CML our primary data format, and take advantage of the already strong support for it in Open Babel. In addition we will be looking at similar optional integration of other libraries such as RDKit, cclib, Chemkit and CDK, and making it easier to integrate functionality developed in other third party libraries we may or may not have access to. Once we have the majority of the core features working in the Avogadro 2 repository we will be moving on to add more advanced functionality such as client-server communication, scaling to large MD simulations and looking at generating more complex input files and ingesting more complex output data. We are already generating nightly binaries automatically on Windows and Mac OS X for those early adopters, but please bear in mind that Avogadro 2 is not yet ready to replace Avogadro 1.x. With that said, I am very excited about the work we are doing, and would welcome feedback from early adopters/ideas and gripes about the way we did things before and better approaches we might take. One major thing that things like MoleQueue offer is the possibility of calling any executable either locally or remotely to perform work, from small things like forcefield geometry optimization to large MD simulations. To that end we are also re-examining how to make scripting and feature additions in Avogadro simpler, so that you can easily generate input for a quantum code without having to touch C++. Over the coming months I will blog about some of these features as we merge them in, and outline our design so that we might get feedback. We are also working with some of the developers of computational codes, CML, and data sets to see how we can address the needs of the community. I will be speaking at FOSDEM in February about our work in the Open Science room, and Bill Hoffman will also be speaking about Open Science in the more general sense as a main track speaker. If you will be there then I would be more than happy to discuss our work with you. Thanks, and happy new year! Marcus ------------------------------------------------------------------------------ Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 _______________________________________________ Avogadro-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/avogadro-devel
