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‎_wikis/3cna.A_2pel.A_cecp.png‎

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‎_wikis/AapropsSkype_20110505.md‎

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title: AapropsSkype 20110505
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---
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Skype call 2011 05 05
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Participants:
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-------------
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Ah Fu, Peter, Andreas
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Installation Issues
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-------------------
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Installation issues, what maven plugins to use ?
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` m2eclipse, m2eclipse-extras, subclipse`
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Mailing list policy
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-------------------
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discuss high level issues on mailing list, technical details in private
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Outlook for this week
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---------------------
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Ah Fu: set up user page on wiki
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Andreas: introduce Ah Fu on mailing list
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Ah Fu:
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- add biojava3-aa-prop module to the top level maven configuration
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file
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- mail biojava-dev for priorities of properties, ask for ideas for any
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new properties
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- develop high level interfaces for the main physico-chemical
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properties
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‎_wikis/AapropsSkype_20110505.mediawiki‎

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Skype call 2011 05 05
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==Participants:==
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Ah Fu, Peter, Andreas
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== Installation Issues ==
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Installation issues, what maven plugins to use ?
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m2eclipse, m2eclipse-extras, subclipse
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== Mailing list policy ==
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discuss high level issues on mailing list, technical details in private
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== Outlook for this week ==
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Ah Fu: set up user page on wiki
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Andreas: introduce Ah Fu on mailing list
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Ah Fu:
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* add biojava3-aa-prop module to the top level maven configuration file
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* mail biojava-dev for priorities of properties, ask for ideas for any new properties
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* develop high level interfaces for the main physico-chemical properties

‎_wikis/AapropsSkype_20110512.md‎

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title: AapropsSkype 20110512
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---
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[back to project](GSoC:AAPropertiesComputation "wikilink")
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Participants:
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-------------
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Ah Fu, Peter, Andreas
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BasicProperties Interface
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-------------------------
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Discussion of BasicProperties interface.
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Next step: Constraints
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----------------------
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What constraints shall we use?
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First approach - code in Java
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Later we will load them from XML
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- important to track where constraints came from

‎_wikis/AapropsSkype_20110512.mediawiki‎

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[[GSoC:AAPropertiesComputation|back to project]]
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== Participants: ==
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Ah Fu, Peter, Andreas
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== BasicProperties Interface ==
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Discussion of BasicProperties interface.
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== Next step: Constraints ==
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What constraints shall we use?
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First approach - code in Java
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Later we will load them from XML
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- important to track where constraints came from

‎_wikis/AapropsSkype_20110519.md‎

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title: AapropsSkype 20110519
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---
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Skype call 2011 05 19
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Participants:
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-------------
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Ah Fu, Peter, apologise from Andreas
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Outlook for this week
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---------------------
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Bad connection on Skype had to preliminary terminate the meeting.
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Ah Fu:
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- write up remaining questions in email
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- correct javadoc
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- start implementing the methods of BasicProperties interface
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- read on about JUnit
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- write test cases for the newly implemented methods
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- try making Google Talk to work as backup option for phone calls
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Peter:
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- address Ah Fu questions
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‎_wikis/AapropsSkype_20110519.mediawiki‎

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Skype call 2011 05 19
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==Participants:==
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Ah Fu, Peter, apologise from Andreas
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== Outlook for this week ==
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Bad connection on Skype had to preliminary terminate the meeting.
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Ah Fu:
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* write up remaining questions in email
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* correct javadoc
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* start implementing the methods of BasicProperties interface
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* read on about JUnit
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* write test cases for the newly implemented methods
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* try making Google Talk to work as backup option for phone calls
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Peter:
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* address Ah Fu questions

‎_wikis/AapropsSkype_20110526.md‎

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title: AapropsSkype 20110526
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---
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Participants:
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-------------
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Ah Fu, Peter, Andreas
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Ah Fu status update
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-------------------
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- do we have an symbol for "unknown" amino acid"
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- isoelectric point calc- what to do if close to 0
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- differences in molecular weight slight differences when compared with
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other site
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ah fu to send by email with more detail
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Peter
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-----
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- suggestions: use Task panel in Eclipse, can be used to address TODO
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comments
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- comment SVN commits
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- add a couple of new methods for easier access for the users
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Outlook for this week
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---------------------
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- work on TODOs in the code
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- develop junit test cases for all the methods
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- mentor input required for validation of methods
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- improve methods

‎_wikis/AapropsSkype_20110526.mediawiki‎

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==Participants:==
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Ah Fu, Peter, Andreas
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== Ah Fu status update ==
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- do we have an symbol for "unknown" amino acid"
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- isoelectric point calc- what to do if close to 0
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- differences in molecular weight slight differences when compared with other site
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ah fu to send by email with more detail
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== Peter ==
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- suggestions: use Task panel in Eclipse, can be used to address TODO comments
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- comment SVN commits
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- add a couple of new methods for easier access for the users
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== Outlook for this week ==
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- work on TODOs in the code
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- develop junit test cases for all the methods
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- mentor input required for validation of methods
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- improve methods

‎_wikis/AapropsSkype_20110602.md‎

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title: AapropsSkype 20110602
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---
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Participants:
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-------------
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Ah Fu, Peter, Andreas
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Ismb
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----
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Peter and Andreas will meet at Ismb Vienna
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Junit tests
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-----------
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We start to have unit tests. They are testing correct usage and results
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of the software. Peter: also add extreme cases for testing in an attempt
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to try to break the API.
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- Equals test for double: precision problem. Solution: round to the
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desired precision. - Execution time of tests - broken tests - can't
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install with Maven
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Exceptions for invalid characters
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---------------------------------
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Shall we throw exceptions for invalid characters or just ignore them?
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If we can fix the problem, we will try to fix it, otherwise we will
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throw exception.
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Javadocs in SVN
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---------------
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ignore in SVN
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Outlook for next week
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---------------------
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break API as part of junit tests
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start working on next properties: solv access sec struc charge
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hydrophobicity
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molecular weight - load from XML to support multiple source

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