Egon Willighagen

[Dan](http://www.openscience.org/blog/) (the original
[Jmol](http://www.jmol.org/) author) has an interesting blog series: How
to make money from Open Source scientific software
[I](http://www.openscience.org/blog/?p=164),
[II](http://www.openscience.org/blog/?p=165) and
[III](http://www.openscience.org/blog/?p=166). Three more blog items are
in the planning. The deal with how to make money from open source
scientific software. He wants to be able to skeptically review the
software in his field, hence open source. But open source software
development, at least in chemistry, needs funding, because there are too
few people working on such software on a voluntary basis.

The articles discuss possible scenarios. Article I discusses 'Sell
hardware' that comes with open source software, and article II discusses
the 'Sell services' scenario, which still works in the GNU/Linux OS
world. He argues that selling support does not fit the chem-bla-ics
world: *"First, scientific software targets a relatively small group of
users, and at the same time, the development and support costs are often
quite large."* and *"Why would a researcher spend \$10000 on a support
contract if the problem could be solved by throwing a graduate student
at the open source version of the code for a few months?"* Interesting
arguments indeed.

Instead, he suggests, the service sold should be knowledge. The open
source based company should sell knowledge, should solve customer
problems using open source software. Each problem will come with
specific needs, allowing indirect funding of open source development.
And, yes, this is indeed how open source chemo-/bioinformatics software
is currently development: as a mean to solve scientific challenging
problems.

I'm looking forward to his next articles in this series.

#### References


Dan (the original Jmol author) has an interesting blog series: How to make money from Open Source scientific software I, II and III. Three more blog items are in the planning. The deal with how to make money from open source scientific software. He wants to be able to skeptically review the software in his field, hence open source.

How to make money from Open Source scientific software

Geldenhuys et al. published an article in [Drug Discovery
Today](http://www.sciencedirect.com/science/journal/13596446) titled
*Optimizing the use of open-source software applications in drug
discovery*
(DOI:[10.1016/S1359-6446(05)03692-5](https://doi.org/10.1016/S1359-6446(05)03692-5)),
and approached the review from a bench chemist point of view.
Unfortunately, he discusses free, but closed source, program in one go.

He discusses the advantages and problems with opensource, and mentions
the often lacking user-friendly GUI (true), and the the lack of
literature to validate the program. It was unclear to me wether the last
argument applied to the free tools, or to the open source programs; I
thought the open-source projects like the [CDK](http://cdk.sf.net/),
[JOELib](http://joelib.sf.net/), [Jmol](http://www.jmol.org/) and
[PyMol](http://pymol.sf.net/) were quite strong in this area, at least
compared to the commercial software I have seen.

#### References

- [10.1016/S1359-6446(05)03692-5](https://doi.org/10.1016/S1359-6446(05)03692-5)


Optimizing the use of open-source software applications in drug discovery

Geldenhuys et al. published an article in Drug Discovery Today titled
<em>
 Optimizing the use of open-source software applications in drug discovery
</em>
(DOI:10.1016/S1359-6446(05)03692-5), and approached the review from a bench chemist point of view.

Open source in drug discovery

OpenSource, OpenData and OpenStandards are not as strong in
chemoinformatics as they are in bioinformatcs, where it is common
knowledge that sharing is a good. Today, the
[JCIM](http://pubs3.acs.org/acs/journals/toc.page?incoden=jcisd8)
published on the web an [article](http://dx.doi.org/10.1021/ci050400b)
about the [Blue Obelisk](http://www.blueobelisk.org/) movement, which
promotes these three idealogies.

Several open source projects participate, amongst which the
[CDK](http://cdk.sf.net/), [Jmol](http://www.jmol.org/),
[JOELib](http://joelib.sf.net/), [OpenBabel](http://openbabel.sf.net/),
[Chemical Markup Language](http://cml.sf.net/),
[Bioclipse](http://bioclipse.net/) and [Kalzium](http://cdk.sf.net/).

#### References

- [10.1021/CI050400B](https://doi.org/10.1021/CI050400B)


The Blue Obelisk—Interoperability in Chemical Informatics

OpenSource, OpenData and OpenStandards are not as strong in chemoinformatics as they are in bioinformatcs, where it is common knowledge that sharing is a good. Today, the JCIM published on the web an article about the Blue Obelisk movement, which promotes these three idealogies. Several open source projects participate, amongst which the CDK, Jmol, JOELib, OpenBabel, Chemical Markup Language, Bioclipse and Kalzium.

BlueObelisk: OpenSource, OpenData and OpenStandards

This is the best news I heard in weeks! The [US Patent and Trade
Offfice](http://www.uspto.gov/) spoke with open source representatives
about ways to deal with open source software as prior art. Apparently,
their problem was how to be sure about release dates of open source, and
authoritative sites like [SourceForge.net](http://www.sf.net/),
[FreshMeat.net](http://freshmeat.net/) help a lot here, which extensive
logging of releases.

Quoting from there website:

:::: {.language-plaintext .highlighter-rouge}
::: {.highlight}
``` highlight
The Department of Commerce’s United States Patent and Trademark Office (USPTO)
has created a partnership with the open source community to ensure that patent
examiners have access to all available prior art relating to software code
during the patent examination process.
```
:::
::::

It also indicates that releasing open source software with, or
announcing it on, such an authoritative website is important! Otherwise,
patent offices will not be able to decide wether our open source art is
really prior.

#### References


This is the best news I heard in weeks! The US Patent and Trade Offfice spoke with open source representatives about ways to deal with open source software as prior art. Apparently, their problem was how to be sure about release dates of open source, and authoritative sites like SourceForge.net, FreshMeat.net help a lot here, which extensive logging of releases.

Rogue Scholar Beiträge

How to make money from Open Source scientific software

Open source in drug discovery

BlueObelisk: OpenSource, OpenData and OpenStandards

USPTO considers open source software prior art