Recent Changes for "First Quixote Conference - 22nd-23rd March 2010" - Quixote project on QC databases

First Quixote Conference - 22nd-23rd March 2010

2011-03-22 14:07:15

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- \|\|9:50-10:10\|\|Q5cost, a possible common format for Quantum Chemistry - [http://hpc.cineca.it/content/elda-rossi Elda Rossi]\|\| [[File(q5cost.pdf)]] - \|\|10:10-10:30\|\|TURBOMOLE and CML - Semi-direct vs. parser approach - [http://www.luethi.ethz.ch/people/gloessa Andreas Gloess]\|\|[[File(talk.pdf)]]	+ \|\|9:50-10:10\|\|Q5cost, a possible common format for Quantum Chemistry - [http://hpc.cineca.it/content/elda-rossi Elda Rossi]\| [[File(q5cost.pdf)]]\|\| + \|\|10:10-10:30\|\|TURBOMOLE and CML - Semi-direct vs. parser approach - [http://www.luethi.ethz.ch/people/gloessa Andreas Gloess]\| [[File(talk.pdf)]]\|\|

First Quixote Conference - 22nd-23rd March 2010

2011-03-22 14:01:49

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- \|\|10:10-10:30\|\|TURBOMOLE and CML - Semi-direct vs. parser approach - [http://www.luethi.ethz.ch/people/gloessa Andreas Gloess]\|\|	+ \|\|10:10-10:30\|\|TURBOMOLE and CML - Semi-direct vs. parser approach - [http://www.luethi.ethz.ch/people/gloessa Andreas Gloess]\|\|[[File(talk.pdf)]]

First Quixote Conference - 22nd-23rd March 2010

2011-03-22 14:01:08

Upload of file talk.pdf.

First Quixote Conference - 22nd-23rd March 2010

2011-03-22 11:40:58

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- \|\|9:50-10:10\|\|Q5cost, a possible common format for Quantum Chemistry - [http://hpc.cineca.it/content/elda-rossi Elda Rossi]\|\|	+ \|\|9:50-10:10\|\|Q5cost, a possible common format for Quantum Chemistry - [http://hpc.cineca.it/content/elda-rossi Elda Rossi]\|\| [[File(q5cost.pdf)]]

First Quixote Conference - 22nd-23rd March 2010

2011-03-22 11:40:27

Upload of file q5cost.pdf.

First Quixote Conference - 22nd-23rd March 2010

JorgeEstrada — 2011-03-22 10:41:22

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	+ + Meeting's EtherPad is at [http://okfnpad.org/quixotemeeting].

First Quixote Conference - 22nd-23rd March 2010

JensThomas — 2011-03-16 16:55:09

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- \|\|8:30\|\|Taxis from Hotel to Lab\|\| - \|\|<rowbgcolor="#D3D3D3">9:00-9:20\|\|Tea/Coffee\|\| - \|\|9:20-9:40\|\|Introduction to Conference and Quixote Project - Jens Thomas\|\| - \|\|9:40-10:00\|\|Q5cost, a possible common format for Quantum Chemistry - [http://hpc.cineca.it/content/elda-rossi Elda Rossi]\|\| - \|\|10:00-10:20\|\|TURBOMOLE and CML - Semi-direct vs. parser approach - [http://www.luethi.ethz.ch/people/gloessa Andreas Gloess]\|\| - \|\|10:20-10:40\|\|Avogadro & Kitware - [http://www.kitware.com/company/team/hanwell.html Marcus Hanwell]\|\| - \|\|10:40-11:00\|\|Quantum Expresso, Moka & XML - [http://www.sissa.it/main/?p=PHONEBOOK&surname=Sabatini&name=Riccardo Riccardo Sabatini]\|\| - \|\|<rowbgcolor="#D3D3D3">11:00-11:15\|\|Tea/Coffee\|\| - \|\|11:15-12:30\|\|Introduction to parsers, dictionaries, CML and databases - [http://www-pmr.ch.cam.ac.uk/wiki/Main_Page Peter Murray-Rust et al.]\|\|	+ \|\|9:00\|\|Taxis from Hotel to Lab\|\| + \|\|<rowbgcolor="#D3D3D3">9:15-9:30\|\|Tea/Coffee\|\| + \|\|9:30-9:50\|\|Introduction to Conference and Quixote Project - Jens Thomas\|\| + \|\|9:50-10:10\|\|Q5cost, a possible common format for Quantum Chemistry - [http://hpc.cineca.it/content/elda-rossi Elda Rossi]\|\| + \|\|10:10-10:30\|\|TURBOMOLE and CML - Semi-direct vs. parser approach - [http://www.luethi.ethz.ch/people/gloessa Andreas Gloess]\|\| + \|\|10:30-10:50\|\|Avogadro & Kitware - [http://www.kitware.com/company/team/hanwell.html Marcus Hanwell]\|\| + \|\|10:50-11:10\|\|Quantum Expresso, Moka & XML - [http://www.sissa.it/main/?p=PHONEBOOK&surname=Sabatini&name=Riccardo Riccardo Sabatini]\|\| + \|\|<rowbgcolor="#D3D3D3">11:10-11:25\|\|Tea/Coffee\|\| + \|\|11:25-12:30\|\|Introduction to parsers, dictionaries, CML and databases - [http://www-pmr.ch.cam.ac.uk/wiki/Main_Page Peter Murray-Rust et al.]\|\|

First Quixote Conference - 22nd-23rd March 2010

2011-03-16 12:12:56

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- \|\|10:00-10:20\|\|TURBOMOLE and CML - Parsers vs. semi-direct approach - [http://www.luethi.ethz.ch/people/gloessa Andreas Gloess]\|\|	+ \|\|10:00-10:20\|\|TURBOMOLE and CML - Semi-direct vs. parser approach - [http://www.luethi.ethz.ch/people/gloessa Andreas Gloess]\|\|

First Quixote Conference - 22nd-23rd March 2010

2011-03-16 12:12:03

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- \|\|10:00-10:20\|\|TURBOMOLE and CML --- Parsers vs. semi-direct approach -[http://www.luethi.ethz.ch/people/gloessa Andreas Gloess]\|\|	+ \|\|10:00-10:20\|\|TURBOMOLE and CML - Parsers vs. semi-direct approach - [http://www.luethi.ethz.ch/people/gloessa Andreas Gloess]\|\|

First Quixote Conference - 22nd-23rd March 2010

2011-03-16 12:11:43

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- \|\|10:00-10:20\|\|[http://www.luethi.ethz.ch/people/gloessa Andreas Gloess]\|\|	+ \|\|10:00-10:20\|\|TURBOMOLE and CML --- Parsers vs. semi-direct approach -[http://www.luethi.ethz.ch/people/gloessa Andreas Gloess]\|\|

First Quixote Conference - 22nd-23rd March 2010

2011-03-16 12:10:29

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- \|\|10:00-10:20\|\|[http://www.luethi.ethz.ch/people/gloessa Andreas Gloss]\|\|	+ \|\|10:00-10:20\|\|[http://www.luethi.ethz.ch/people/gloessa Andreas Gloess]\|\|

First Quixote Conference - 22nd-23rd March 2010

JensThomas — 2011-03-16 11:17:33

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- \|\|Arrival at Daresbury Park Hotel \|\| \|\|	+ \|\|\|\|Arrival at Daresbury Park Hotel - check-in from 15:00 \|\|
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- \|\|<rowbgcolor="#D3D3D3">9:00-9:30\|\|Tea/Coffee\|\| - \|\|9:30-11:00\|\|Talks\|\|	+ \|\|<rowbgcolor="#D3D3D3">9:00-9:20\|\|Tea/Coffee\|\| + \|\|9:20-9:40\|\|Introduction to Conference and Quixote Project - Jens Thomas\|\| + \|\|9:40-10:00\|\|Q5cost, a possible common format for Quantum Chemistry - [http://hpc.cineca.it/content/elda-rossi Elda Rossi]\|\| + \|\|10:00-10:20\|\|[http://www.luethi.ethz.ch/people/gloessa Andreas Gloss]\|\| + \|\|10:20-10:40\|\|Avogadro & Kitware - [http://www.kitware.com/company/team/hanwell.html Marcus Hanwell]\|\| + \|\|10:40-11:00\|\|Quantum Expresso, Moka & XML - [http://www.sissa.it/main/?p=PHONEBOOK&surname=Sabatini&name=Riccardo Riccardo Sabatini]\|\|
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- \|\|11:15-12:30\|\|Talks\|\|	+ \|\|11:15-12:30\|\|Introduction to parsers, dictionaries, CML and databases - [http://www-pmr.ch.cam.ac.uk/wiki/Main_Page Peter Murray-Rust et al.]\|\|
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- \|\|<rowbgcolor="#D3D3D3">19:00\|\|Dinner at the Ring o'Bells\|\|	+ \|\|<rowbgcolor="#D3D3D3">19:00\|\|Dinner at the Ring O'Bells\|\|

First Quixote Conference - 22nd-23rd March 2010

2011-03-09 14:14:43

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	+ \|\|8:30\|\|Taxis from Hotel to Lab\|\|
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	+ \|\|8:30\|\|Taxis from Hotel to Lab\|\|

First Quixote Conference - 22nd-23rd March 2010

JensThomas — 2011-03-08 11:56:53

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	+ + === Contact === + + For further information about the meeting, or if you are interested in attending, please contact Jens Thomas: jens.thomas@stfc.ac.uk

First Quixote Conference - 22nd-23rd March 2010

JensThomas — 2011-03-07 16:55:01

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	+ === Timetable === + + '''NB:''' - this is a draft timetable and subject to change. + + \|\|\|\|'''Monday 21st March'''\|\| + \|\|Arrival at Daresbury Park Hotel \|\| \|\| + \|\|\|\|'''Tuesday 22nd March'''\|\| + \|\|'''Time'''\|\|'''Activity'''\|\| + \|\|<rowbgcolor="#D3D3D3">9:00-9:30\|\|Tea/Coffee\|\| + \|\|9:30-11:00\|\|Talks\|\| + \|\|<rowbgcolor="#D3D3D3">11:00-11:15\|\|Tea/Coffee\|\| + \|\|11:15-12:30\|\|Talks\|\| + \|\|<rowbgcolor="#D3D3D3">12:30-13:30\|\|Lunch\|\| + \|\|13:30-15:30\|\|Work on parsers/database\|\| + \|\|<rowbgcolor="#D3D3D3">15:30-15:45\|\|Tea/Coffee\|\| + \|\|15:45-18:30\|\|Work on parsers/database\|\| + \|\|<rowbgcolor="#D3D3D3">19:00\|\|Dinner at the Ring o'Bells\|\| + \|\|\|\|'''Wednesday 23rd March'''\|\| + \|\|'''Time'''\|\|'''Activity'''\|\| + \|\|<rowbgcolor="#D3D3D3">9:00-9:30\|\|Tea/Coffee\|\| + \|\|9:30-11:00\|\|Work on parsers/database\|\| + \|\|<rowbgcolor="#D3D3D3">11:00-11:15\|\|Tea/Coffee\|\| + \|\|11:15-12:30\|\|Work on parsers/database\|\| + \|\|<rowbgcolor="#D3D3D3">12:30-13:30\|\|Lunch\|\| + \|\|13:30-15:00\|\|Work on parsers/database\|\| + \|\|<rowbgcolor="#D3D3D3">15:00-15:15\|\|Tea/Coffee\|\| + \|\|15:15-16:30\|\|Work on parsers/database\|\| + \|\|16:30-17:00\|\|Summing up\|\| + +

First Quixote Conference - 22nd-23rd March 2010

JensThomas — 2011-03-02 10:42:06

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	+ --> '''Sponsored by the [http://www.cse.scitech.ac.uk/events/Hartree_Summary/ Hartree Centre]''' <--

First Quixote Conference - 22nd-23rd March 2010

JensThomas — 2011-03-02 10:26:51

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	+ + For a general overview of the Quixote Project, please follow the links on the ["Front Page"]. +

First Quixote Conference - 22nd-23rd March 2010

JensThomas — 2011-03-02 10:14:01

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- A meeting to create the first Open distributed repository for electronic simulations.	+ [[br]] + --> '''A meeting to create the first Open distributed repository for electronic simulations''' <-- + [[br]]
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- The meeting will take place at [http://www.stfc.ac.uk/About%20STFC/45.aspx STFC Daresbury Laboratory].	+ [[TableOfContents]]
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- For invited attendees, accommodation has been arranged for the nights of the 21st and 22nd at the [http://www.devere.co.uk/our-locations/daresbury-park.html Daresbury Park Hotel]	+ === Goals === + * '''Primary:''' build and populate a Chempound repository for outputs from electronic codes. Repository should search for chemical concepts, job meta-data and core physico-chemical properties. + * '''Subsidiary:''' build Core CML-XML parsers for 3- 8 commonly used codes in atomistic QM and planewave simulations. Use Lensfield to scrape directories for files.
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- ==== Goals ==== - * main: build and populate a Chempound repository for outputs from electronic codes. Repository should search for chemical concepts, job metadata and core physicochemical properties. - * subsidiary: build Core CML-XML parsers for 3- 8 commonly used codes in atomistic QM and planewave simulations. Use Lensfield to scrape directories for files.	+ === Emphasis === + * Chemistry (not QM methodology). + * practical achievement (running code and a working repository). + * Opensource/opendata without access control to the repository. Repoistry-agnostic (?[http://swordapp.org/ SWORD],?[http://www.openarchives.org/ore/ OAI])
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- ==== Emphasis ==== - * Chemistry (not QM methodology). - * practical achievement (running code and working repository). - * (Opensource)/opendata without access control to repo. Repo-agnostic (?SWORD,?OAI) - - - ==== Technologies ==== - * Lensfield - * JUMBO - * Moka - * Avogadro - * Chempound	+ === Structure ===
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- === Strand 1 - ChemPound === - * use case: searching repo for given concept over several filetypes - * preparation: several CML files (with index data) for several codes	+ ==== Strand 1 - ChemPound ==== + * '''use case:''' searching the repository for given concept over several filetypes + * '''preparation:''' several CML files (with index data) for several codes
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- === Strand 2 - Lensfield, JUMBOConverters ===	+ ==== Strand 2 - Lensfield, JUMBOConverters ====
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	+ + ==== Technologies ==== + * ["Lensfield2"] + * ["JUMBO"] + * Moka + * [http://avogadro.openmolecules.net Avogadro] + * Chempound + + === Venue and Travel === + + The meeting will take place at [http://www.stfc.ac.uk/About%20STFC/45.aspx STFC Daresbury Laboratory]. + + The closest airports are [http://www.manchesterairport.co.uk/to-and-from-airport/ Manchester] and [http://www.liverpoolairport.com/getting-to/from-airport.html Liverpool]. + + For invited attendees, accommodation has been arranged for the nights of the 21st and 22nd at the [http://www.devere.co.uk/our-locations/daresbury-park.html Daresbury Park Hotel]

First Quixote Conference - 22nd-23rd March 2010

JensThomas — 2011-02-28 11:01:14

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	+ + For invited attendees, accommodation has been arranged for the nights of the 21st and 22nd at the [http://www.devere.co.uk/our-locations/daresbury-park.html Daresbury Park Hotel]

First Quixote Conference - 22nd-23rd March 2010

JensThomas — 2011-02-28 10:25:56

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- Goals:	+ ==== Goals ====
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- Emphasis:	+ ==== Emphasis ====
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	+ + ==== Technologies ==== + * Lensfield + * JUMBO + * Moka + * Avogadro + * Chempound
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	+ + * The codes should all have mini-dictionaries (some will be large) + * The indexes will be normalized (e.g. dates, units, formulae, etc.). This means that users search a single conceptual model but the original data is not affected and can be retrieved as part of the ORE aggregation.

First Quixote Conference - 22nd-23rd March 2010

JensThomas — 2011-02-28 10:22:51

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	+ = CML-XML Quixote Meeting 22nd-23rd March STFC Daresbury Laboratory = + + A meeting to create the first Open distributed repository for electronic simulations. + + The meeting will take place at [http://www.stfc.ac.uk/About%20STFC/45.aspx STFC Daresbury Laboratory]. + + Goals: + * main: build and populate a Chempound repository for outputs from electronic codes. Repository should search for chemical concepts, job metadata and core physicochemical properties. + * subsidiary: build Core CML-XML parsers for 3- 8 commonly used codes in atomistic QM and planewave simulations. Use Lensfield to scrape directories for files. + + Emphasis: + * Chemistry (not QM methodology). + * practical achievement (running code and working repository). + * (Opensource)/opendata without access control to repo. Repo-agnostic (?SWORD,?OAI) + + + The meeting will have two main strands: + + === Strand 1 - ChemPound === + * use case: searching repo for given concept over several filetypes + * preparation: several CML files (with index data) for several codes + * Files for data set (final CML, original TXT, index.rdf, etc.) aggregated under ORE + * Aggregation uploaded by SWORD (METS, ZIP, etc.. as agreed) + * index in simple name-value search (?RDF, ?Mongo) + + === Strand 2 - Lensfield, JUMBOConverters === + * Use-case: disk populated with calculations of given kind where (say) suffix = FOO . + * Arbitrary directory structure. + * Lensfield trawls disk for .foo + JumboFooConverter/Parser converts to CML (failures => null files). + * conversion supported by FooDict.cml + + The parsing need not be complete. The CML is used for specific data and indexing. The results COULD (if all goes well) be fed into the Chempound repo. + Small Parsers can be written on-the-fly for codes if the format is pre-explored. We do not have to do the whole job.