Chem4Word – aspects of Openness

I’ll now reply to the second part of Rich’s question

Metallocenes? Axial Chirality? Apache/MIT/BSD License? OpenOffice? GitHub?

My current understanding is that C4W will be posted on CodePlex when we believe it’s in a reasonable state for community work. Good Open Source projects need clear release management and we haven’t yet addressed that, but we shall. I’m not very familiar with CodePlex but it tells me:

CodePlex is Microsoft’s open source project hosting web site. Start a new project, join an existing one, or download software created by the community.


Microsoft is hosting the CodePlex site solely as a web storage site as a service to the developer community

From WP I find:

CodePlex is an open source project hosting website from Microsoft. It allows shared development of open source software. Its features include wiki pages, source control based on Team Foundation Server but accessible using Subversion, discussion forums, issue tracking, project tagging, RSS support, statistics, and releases. Some of the available licenses are more restrictive than traditional open source licenses[1].

Choosing an Open Source licence is not trivial, and we haven’t yet chosen one. We’d welcome informed comment. The site offers, inter alia, Apache 2.0 and MsPL. JUMBO is Artistic because it allowed me to require forkers to rename and acknowledge. It’s compatible with MS Open philosophy. Much of the Blue Obelisk is LGPL which is probably compatible. Open Babel is GPL, probably incompatible with Microsoft licences.

Open Office? This probably relates to interoperability between the two systems. There are several aspects; some interoperates and some doesn’t. I’m visiting Peter Sefton in Toowoomba this month and we’ll probably find out what works and what doesn’t. Peter has managed to get CML molecules into ICE/ODT and interoperating with Open Office, but I don’t know the details. But as a rough guide I’d say:

  • The C4W code is C# so only works in a environment that supports that. There are Open C# implementations, but I have no idea what they are like. I would doubt it suport the UI and graphics.
  • WPF and XAML. Probably not interoperable. But I know of no high-quality graphics/UI system that is truly interoperable.
  • customXML (where the CML is). I don’t know details, and I suspect they are somewhat hairy, but the CML itself is unaffected.
  • OOXML and ODT. I suspect these are interoperable enough for most chemistry purposes.

GitHub. WP says:

GitHub is a web-based hosting service for projects that use the Git revision control system. It is written in Ruby on Rails by Logical Awesome developers Chris Wanstrath, PJ Hyett, and Tom Preston-Werner. GitHub offers both commercial plans and free accounts for open source projects. It is similar to Bitbucket which uses Mercurial.

I’m not sure how this is relevant. Currently we mainly use Subversion on Sourceforge, but Nico has mounted his ontology on BitBucket and I am sure he’ll tell us about it. We haven’t decided on the developer strategy yet but I would expect a single point of contact will work initially. I haven’t found MS’s TFS very cuddly yet and I prefer Subversion, but I am sure all these systems will develop.

This entry was posted in Uncategorized. Bookmark the permalink.

3 Responses to Chem4Word – aspects of Openness

  1. Rich Apodaca says:

    >Open Babel is GPL, probably incompatible with Microsoft licences.
    Which Microsoft licenses and incompatible how? Up until now I was thinking of C4W as a Word plug-in independently downloaded/installed and therefore in principle independent of any Microsoft licensing.
    Regarding OpenOffice, the question is really how tightly coupled C4W is to the Microsoft Word format? Organizations around the world are under increasing budgetary pressure to drop Word in favor of free alternatives (OpenOffice being a popular one). I haven’t kept up with all of the back and forth between MS and, but it sounded like there was some incompatibility between the two XML formats. Maybe it’s no longer a big deal – I have no idea.
    How deep are these differences and how difficult would they make it to embed chunks of C4W into OO documents (disregarding the issue of creating an OO plugin to do anything with the embedded C4W)?

  2. pm286 says:

    My previous replies have been trashed (by WordPress) so am brief.
    p1. You can do anything you like. We can probably not integrate OB into our distro.
    p2. Addressed in other posts.
    p3. I think you mean “merge OOXML with ODT”. Don’t know but will be trying.

  3. Pingback: The Microsoft Biology Foundation « Semantic Science

Leave a Reply

Your email address will not be published. Required fields are marked *