Questions and answers for compchem problems (?Shapado)
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Peter Murray-Rust
Jun 5, 2011, 6:24:32 AM6/5/11
to BlueObelisk-Discuss, Quixote mail list
**Copied to both Blue Obelisk and Quixote lists. please be careful in replying to both and please keep to topic **
Background
=========
The Quixote project (http://quixote.wikispot.org/) is an Open Source/Data project to create and capture compchem calculations in semantic form and make them available Openly to all. We have now (Friday) released our prototype repository at: http://quixote.ch.cam.ac.uk/content/index.html We expect this to include tens of thousands of contributed logfiles and their semantic (CML) comversions. There is already feedback and questions being asked.
The Blue Obelisk (http://sourceforge.net/apps/mediawiki/blueobelisk/index.php?title=Main_Page) has created and maintains many major Open Source codes and Open Data/Open Standards resources. It has set up a site http://blueobelisk.shapado.com/ where anyone can ask and answer questions on Open (Data/Source/Standards). This has proven its worth and has many contributors. The software is an Open version of the very successful Stack Overflow (etc.) sites for software questions (http://stackoverflow.com/ )
Requirement
==========
Many people involved in compchem (users, consumers, coders, interfacers, etc.) have questions that cannot be easily answered. There are many reasons:
* novice status - don't know where to look or who to ask
* unexpected program behaviour (PMR had this with GAMESS-US - lines > 80 chars corrupt silently)
* undocumented behaviour or output
* questions about strategy
etc.
Here are some questions I would like to ask:
* why are there only 7 Fukui components in NWChem (I expected 8)?
* what does "Stoichiometry" mean in Gaussian logfiles?
* what level of optimization is required before calculating 13C NMR shifts?
* why does this GAMESS-US input fail to give the right number of atoms?
* can NWChem calculate chemical shifts?
* which open Source codes do QMMM?
Shapado approach
===============
Although Open sites in chemistry have very variable uptake I think that compchem is an exception and will work extremely well.
* its scope is well-bounded (it's relatively easy to see whether something is compchem or not)
* there is a very large number of practitioners at all levels (undergraduate, method user, method developer, central facility - e.g. Grid, supercomputer)
* there are tens of millions of jobs run each year
There are several very well understood axes of classification (by method, by basis, by code, by strategy, by compound type, etc .). Therefore is is relatively easy to see which questions nave already been asked? It's easy to browse through (say) all the GAMESS-UK questions.
StackOverflow is incredibly powerful and I get answers with minutes. Here's an example from PMR (http://stackoverflow.com/questions/5879546/parsing-dates-with-variable-spaces ). I think we could fairly soon get a critical mass of questions and answers. The SO experience shows that it covers the whole area from undergraduate to unaswered research problems (there's a convention that "homework" questions are treated sympathetically but that you don't give the full answer to start with ("plz send me teh codez")).
Proposal
=======
We create a Shapado for computational chemistry (QC, MD and similar) which answers any questions (not just those on Open Source). [I am assuming this does not already exist]. The Openness comes from the Open discussion and the desire to create Open practices and resources but it should follow the SO practice that any codes, any data, any workplace is welcome. (Product information in response to genuine questions is allowed but not product placement - advertising). It must be Open in that the site should not be "closable" later as happens with many free-as-in-beer sites. I am assuming that it will have a good membership of BO+Q members but anyone can play.
Action
=====
We need to know what is involved in setting up such a site and running it. I know that Egon has been heavily involved - who else. I'm guessing that there would be Quixotans who can get started.
As long as your mails are in scope of this question and the way forward is being debated it's probably a good idea to copy both lists. There will come a time when we need to change this.
P.
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
Background
=========
The Quixote project (http://quixote.wikispot.org/) is an Open Source/Data project to create and capture compchem calculations in semantic form and make them available Openly to all. We have now (Friday) released our prototype repository at: http://quixote.ch.cam.ac.uk/content/index.html We expect this to include tens of thousands of contributed logfiles and their semantic (CML) comversions. There is already feedback and questions being asked.
The Blue Obelisk (http://sourceforge.net/apps/mediawiki/blueobelisk/index.php?title=Main_Page) has created and maintains many major Open Source codes and Open Data/Open Standards resources. It has set up a site http://blueobelisk.shapado.com/ where anyone can ask and answer questions on Open (Data/Source/Standards). This has proven its worth and has many contributors. The software is an Open version of the very successful Stack Overflow (etc.) sites for software questions (http://stackoverflow.com/ )
Requirement
==========
Many people involved in compchem (users, consumers, coders, interfacers, etc.) have questions that cannot be easily answered. There are many reasons:
* novice status - don't know where to look or who to ask
* unexpected program behaviour (PMR had this with GAMESS-US - lines > 80 chars corrupt silently)
* undocumented behaviour or output
* questions about strategy
etc.
Here are some questions I would like to ask:
* why are there only 7 Fukui components in NWChem (I expected 8)?
* what does "Stoichiometry" mean in Gaussian logfiles?
* what level of optimization is required before calculating 13C NMR shifts?
* why does this GAMESS-US input fail to give the right number of atoms?
* can NWChem calculate chemical shifts?
* which open Source codes do QMMM?
Shapado approach
===============
Although Open sites in chemistry have very variable uptake I think that compchem is an exception and will work extremely well.
* its scope is well-bounded (it's relatively easy to see whether something is compchem or not)
* there is a very large number of practitioners at all levels (undergraduate, method user, method developer, central facility - e.g. Grid, supercomputer)
* there are tens of millions of jobs run each year
There are several very well understood axes of classification (by method, by basis, by code, by strategy, by compound type, etc .). Therefore is is relatively easy to see which questions nave already been asked? It's easy to browse through (say) all the GAMESS-UK questions.
StackOverflow is incredibly powerful and I get answers with minutes. Here's an example from PMR (http://stackoverflow.com/questions/5879546/parsing-dates-with-variable-spaces ). I think we could fairly soon get a critical mass of questions and answers. The SO experience shows that it covers the whole area from undergraduate to unaswered research problems (there's a convention that "homework" questions are treated sympathetically but that you don't give the full answer to start with ("plz send me teh codez")).
Proposal
=======
We create a Shapado for computational chemistry (QC, MD and similar) which answers any questions (not just those on Open Source). [I am assuming this does not already exist]. The Openness comes from the Open discussion and the desire to create Open practices and resources but it should follow the SO practice that any codes, any data, any workplace is welcome. (Product information in response to genuine questions is allowed but not product placement - advertising). It must be Open in that the site should not be "closable" later as happens with many free-as-in-beer sites. I am assuming that it will have a good membership of BO+Q members but anyone can play.
Action
=====
We need to know what is involved in setting up such a site and running it. I know that Egon has been heavily involved - who else. I'm guessing that there would be Quixotans who can get started.
As long as your mails are in scope of this question and the way forward is being debated it's probably a good idea to copy both lists. There will come a time when we need to change this.
P.
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
Egon Willighagen
Jun 5, 2011, 6:42:41 AM6/5/11
to quixot...@googlegroups.com, BlueObelisk-Discuss
Hi all,
On Sun, Jun 5, 2011 at 12:24 PM, Peter Murray-Rust <pm...@cam.ac.uk> wrote:
> Action
> =====
> We need to know what is involved in setting up such a site and running it. I
> know that Egon has been heavily involved - who else. I'm guessing that there
> would be Quixotans who can get started.
>
> As long as your mails are in scope of this question and the way forward is
> being debated it's probably a good idea to copy both lists. There will come
> a time when we need to change this.
I think the example questions you posted are all suitable for the
existing Blue Obelisk eXchange (BOx). This Q&A is more general about
chemistry, and not about quantum chemistry in particular, but proper
tagging can overcome that, I think.
The questions and answers vary in quality, and its community is
currently not sure about when to jump in and improve existing
questions. Additionally, it's hard to develop a community where people
vote up and down questions actively. Even getting people answering to
up or downvote a question is tricky.
However, on the bright site, it's not just the known Blue Obelisk
addicts who reply. We do have answers showing how closed source tools
fit in. Indeed, the BOx is also about what ODOSOS tools cannot do yet,
and how closed and open tools fit into the mixed environments.
(Seriously, if we start complaining about Blue Obelisk developers
using proprietary tools (I known of none who are 100% Open), we'd get
nowhere. They who are without any closed source tool, cast the first
stone.)
Summarizing, the Quixote community would be most welcome to hang out
on the BOx. If this requires updating texts about the site, let's
discuss that.
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
Peter Murray-Rust
Jun 5, 2011, 7:08:59 AM6/5/11
to quixot...@googlegroups.com, BlueObelisk-Discuss
Thanks Egon,
The "FAQ" states:
I think this would rule out the majority of questions that the wider compchem community would ask as they would not involved any OD/OS/OS at all.
Can you expand on this?
No-one is suggesting that the BO operates as religious Open source (In the OKF we do have people who refuse to use Skype for discussing Open projects and this makes communication difficult).
If I search the tag "software" I get 6 replies (why is the tag only marked X1?)
The first 4 are ODOSOS questions, Coupled with the FAQ I think anyone visiting the site is likely to assume it's only for ODOSOS.
I don't think the current site can evolve seamlessly into something that supports compchem in general - because it will also have to support all sorts of other topics. So the options are:
* create a separate site
* rebrand the existing one
* (possibly) split the current one (though I don't know how).
We only really get one chance at this so we should do it well. I'm neutral but I'll like to see the arguments
P.
I think the example questions you posted are all suitable for the
existing Blue Obelisk eXchange (BOx). This Q&A is more general about
chemistry, and not about quantum chemistry in particular, but proper
tagging can overcome that, I think.
The "FAQ" states:
"The Blue Obelisk Exchange is the place to ask about the use and
development of Open Data, Open Source, and Open Standards: how to
perform tasks and solve chemical problems with these, or if an ODOSOS
tools is available for some task. Or even to ask if someone can provide
such a tool. The questions do not require to be about Blue Obelisk
solutions itself; they can be about any ODOSOS chemistry tool, service,
or database.
I think this would rule out the majority of questions that the wider compchem community would ask as they would not involved any OD/OS/OS at all.
The questions and answers vary in quality, and its community is
currently not sure about when to jump in and improve existing
questions. Additionally, it's hard to develop a community where people
vote up and down questions actively. Even getting people answering to
up or downvote a question is tricky.
Can you expand on this?
However, on the bright site, it's not just the known Blue Obelisk
addicts who reply. We do have answers showing how closed source tools
fit in. Indeed, the BOx is also about what ODOSOS tools cannot do yet,
and how closed and open tools fit into the mixed environments.
(Seriously, if we start complaining about Blue Obelisk developers
using proprietary tools (I known of none who are 100% Open), we'd get
nowhere. They who are without any closed source tool, cast the first
stone.)
No-one is suggesting that the BO operates as religious Open source (In the OKF we do have people who refuse to use Skype for discussing Open projects and this makes communication difficult).
Summarizing, the Quixote community would be most welcome to hang out
on the BOx. If this requires updating texts about the site, let's
discuss that.
If I search the tag "software" I get 6 replies (why is the tag only marked X1?)
Can anyone suggest a good (free) program for viewing SDF files?
Are there any ODOSOS tools for predicting the products of chemical reactions?
Are there any ODOSOS tools for quantum mechanical calculations?
Is there a free toolkit to generate images of chemical reactions from Python
Software for calculation protein-protein interaction
Which (open) electronic lab notebook (ELN) tools do you use?
Are there any ODOSOS tools for predicting the products of chemical reactions?
Are there any ODOSOS tools for quantum mechanical calculations?
Is there a free toolkit to generate images of chemical reactions from Python
Software for calculation protein-protein interaction
Which (open) electronic lab notebook (ELN) tools do you use?
The first 4 are ODOSOS questions, Coupled with the FAQ I think anyone visiting the site is likely to assume it's only for ODOSOS.
I don't think the current site can evolve seamlessly into something that supports compchem in general - because it will also have to support all sorts of other topics. So the options are:
* create a separate site
* rebrand the existing one
* (possibly) split the current one (though I don't know how).
We only really get one chance at this so we should do it well. I'm neutral but I'll like to see the arguments
P.
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
Peter Murray-Rust
Jun 5, 2011, 8:56:33 AM6/5/11
to rajars...@gmail.com, BlueObelisk-Discuss, Quixote mail list
On Sun, Jun 5, 2011 at 12:41 PM, Rajarshi Guha <rajars...@gmail.com> wrote:
On Sun, Jun 5, 2011 at 6:24 AM, Peter Murray-Rust <pm...@cam.ac.uk> wrote:
> Proposal
> =======
> We create a Shapado for computational chemistry (QC, MD and similar) which
> answers any questions (not just those on Open Source). [I am assuming this
> does not already exist]. The Openness comes from the Open discussion and the
> desire to create Open practices and resources but it should follow the SO
> practice that any codes, any data, any workplace is welcome. (Product
> information in response to genuine questions is allowed but not product
> placement - advertising). It must be Open in that the site should not be
> "closable" later as happens with many free-as-in-beer sites. I am assuming
> that it will have a good membership of BO+Q members but anyone can play.
I think Noel had initiated a proposal on StackOverflow for a new Q&A
site for comp chem.
Look forward to hearing Noel's views
But, doesn't the CCL fulfil this need, albeit in a clunky way?
I don't by default want to *compete* against CCL and Jan has done a useful service to the community. However there are some features and styles in CCL which are very different from what we are proposing. There is a difference in a mailing list run by a single person (CCL is a for-profit site) and a community driven site. The list does not allow searching (you have to use Google) and (unless I have missed it) there is no way to follow the discussion after a question has been asked. There is also a lot of stuff which isn't relevant to questions (meetings, product announcements, etc.). I would expect that an SO-like site would bring in new people and make it easier to find and browse answers to and comment on questions.
My motivation also includes:
* something that helps to grow and promote a community
* something that helps to spread Q and BO to a wider audience.
P.
My motivation also includes:
* something that helps to grow and promote a community
* something that helps to spread Q and BO to a wider audience.
P.
Noel O'Boyle
Jun 5, 2011, 9:15:04 AM6/5/11
to Peter Murray-Rust, rajars...@gmail.com, BlueObelisk-Discuss, Quixote mail list
On 5 June 2011 13:56, Peter Murray-Rust <pm...@cam.ac.uk> wrote:
>
>
> On Sun, Jun 5, 2011 at 12:41 PM, Rajarshi Guha <rajars...@gmail.com>
> wrote:
>>
>> On Sun, Jun 5, 2011 at 6:24 AM, Peter Murray-Rust <pm...@cam.ac.uk> wrote:
>>
>> > Proposal
>> > =======
>> > We create a Shapado for computational chemistry (QC, MD and similar)
>> > which
>> > answers any questions (not just those on Open Source). [I am assuming
>> > this
>> > does not already exist]. The Openness comes from the Open discussion and
>> > the
>> > desire to create Open practices and resources but it should follow the
>> > SO
>> > practice that any codes, any data, any workplace is welcome. (Product
>> > information in response to genuine questions is allowed but not product
>> > placement - advertising). It must be Open in that the site should not be
>> > "closable" later as happens with many free-as-in-beer sites. I am
>> > assuming
>> > that it will have a good membership of BO+Q members but anyone can play.
>>
>> I think Noel had initiated a proposal on StackOverflow for a new Q&A
>> site for comp chem.
>
> Look forward to hearing Noel's views
>
>
> On Sun, Jun 5, 2011 at 12:41 PM, Rajarshi Guha <rajars...@gmail.com>
> wrote:
>>
>> On Sun, Jun 5, 2011 at 6:24 AM, Peter Murray-Rust <pm...@cam.ac.uk> wrote:
>>
>> > Proposal
>> > =======
>> > We create a Shapado for computational chemistry (QC, MD and similar)
>> > which
>> > answers any questions (not just those on Open Source). [I am assuming
>> > this
>> > does not already exist]. The Openness comes from the Open discussion and
>> > the
>> > desire to create Open practices and resources but it should follow the
>> > SO
>> > practice that any codes, any data, any workplace is welcome. (Product
>> > information in response to genuine questions is allowed but not product
>> > placement - advertising). It must be Open in that the site should not be
>> > "closable" later as happens with many free-as-in-beer sites. I am
>> > assuming
>> > that it will have a good membership of BO+Q members but anyone can play.
>>
>> I think Noel had initiated a proposal on StackOverflow for a new Q&A
>> site for comp chem.
>
> Look forward to hearing Noel's views
This was not initiated by me, but I've signed up to support it:
http://area51.stackexchange.com/proposals/19727/computational-natural-sciences
They keep changing the scope (feature creep), so that now it includes
comp biol, phys too. I think that's a mistake. Comp chem will be
swamped out. Not enough people have signed up to support it yet, so I
don't know if it's going to make it out of beta.
- Noel
Peter Murray-Rust
Jun 5, 2011, 9:38:44 AM6/5/11
to quixot...@googlegroups.com, rajars...@gmail.com, BlueObelisk-Discuss
On Sun, Jun 5, 2011 at 2:15 PM, Noel O'Boyle <baoil...@gmail.com> wrote:
>This was not initiated by me, but I've signed up to support it:
> Look forward to hearing Noel's views
http://area51.stackexchange.com/proposals/19727/computational-natural-sciences
They keep changing the scope (feature creep), so that now it includes
comp biol, phys too. I think that's a mistake. Comp chem will be
swamped out. Not enough people have signed up to support it yet, so I
don't know if it's going to make it out of beta.
The barrier to adoption is quite high (ca 15 Q's per day, etc - see the physics one http://physics.stackexchange.com/ ). I don't think we ca afford to wait for stackexchange to generate a compchem resource (it's 11% of the way there). And I think - like you - that natural science is far too broad.
For interest, has there been any interaction of this with CCL?
P.
For interest, has there been any interaction of this with CCL?
P.
- Noel
Noel O'Boyle
Jun 5, 2011, 2:49:27 PM6/5/11
to Peter Murray-Rust, quixot...@googlegroups.com, BlueObelisk-Discuss
On 5 June 2011 14:38, Peter Murray-Rust <pm...@cam.ac.uk> wrote:
>
>
> On Sun, Jun 5, 2011 at 2:15 PM, Noel O'Boyle <baoil...@gmail.com> wrote:
>>
>> >
>> > Look forward to hearing Noel's views
>>
>> This was not initiated by me, but I've signed up to support it:
>>
>> http://area51.stackexchange.com/proposals/19727/computational-natural-sciences
>>
>> They keep changing the scope (feature creep), so that now it includes
>> comp biol, phys too. I think that's a mistake. Comp chem will be
>> swamped out. Not enough people have signed up to support it yet, so I
>> don't know if it's going to make it out of beta.
>>
> The barrier to adoption is quite high (ca 15 Q's per day, etc - see the
> physics one http://physics.stackexchange.com/ ). I don't think we ca afford
> to wait for stackexchange to generate a compchem resource (it's 11% of the
> way there). And I think - like you - that natural science is far too broad.
>
>
> On Sun, Jun 5, 2011 at 2:15 PM, Noel O'Boyle <baoil...@gmail.com> wrote:
>>
>> >
>> > Look forward to hearing Noel's views
>>
>> This was not initiated by me, but I've signed up to support it:
>>
>> http://area51.stackexchange.com/proposals/19727/computational-natural-sciences
>>
>> They keep changing the scope (feature creep), so that now it includes
>> comp biol, phys too. I think that's a mistake. Comp chem will be
>> swamped out. Not enough people have signed up to support it yet, so I
>> don't know if it's going to make it out of beta.
>>
> The barrier to adoption is quite high (ca 15 Q's per day, etc - see the
> physics one http://physics.stackexchange.com/ ). I don't think we ca afford
> to wait for stackexchange to generate a compchem resource (it's 11% of the
> way there). And I think - like you - that natural science is far too broad.
> For interest, has there been any interaction of this with CCL?
Well, it was posted to CCL
(http://www.ccl.net/chemistry/resources/messages/2010/09/17.004-dir/index.html).
> P.
>
>> - Noel
>
>
>
> --
> Peter Murray-Rust
> Reader in Molecular Informatics
> Unilever Centre, Dep. Of Chemistry
> University of Cambridge
> CB2 1EW, UK
> +44-1223-763069
>
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