Difference between revisions of "Hackathon 2013/BestPractices"

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Here is our working google doc: [http://wiki.taxonworks.org/index.php?title=Hackathon_2013/BestPractices&action=edit&redlink=1]
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What we did:
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Assessed other taxonomic workbenches, past and present, to try to ID reasons for success/sunsetting, and then glean best practices/things to look out for as a result.
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Overall the systems that have been developed seem to fall victim to funding fall-through and shifting of focus and leadership.  The systems that have survived seem to be:
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* open source and free
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* developed by or in coordination with practicing taxonomists
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* have steady funding or support (i.e. independent of other grants or projects)
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* are modular and support later changes in design and alteration (Diversity Workbench and Scratchpads in particular)
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* are designed to support collaboration between multiple people (this isn't necessarily something that is required for success, though -- however it's interesting that they seem to be designed for use cases that require collaboration at a distance)
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* seem to be cloud-based, though am unclear on that for a few of them
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* note: couldn’t look at ITIS taxonomic workbench because of gov’t shut down.
 +
 
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Basic best practices and system needs from conversation with Lisa:
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* must provide offline access to data (so entirely cloud based is not great)
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* support rapid data entry (either through import or clear and easy support of transcription)
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* should be able to search from other repositories (GenBank)
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* available on one machine (again, cloud based is not great)
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* must support publication workflow (thus, good reference management modules are important)
 +
* need to be able to hook into institutional specimen databases (depending on workflow.  This means that a workbench either needs to be a solution for tricky institutional database setups (e.g. idiosyncratic DBS or convoluted KE Emu set ups), or something that can work alongside them)
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* for systematists, should fit into existing/common bioinformatics pipelines
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 +
 
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Here is our working google doc: [https://docs.google.com/document/d/14cJvWjdneQMIcO3RfS_EEDpethQXZcmY5VII1GruFwY/edit?usp=sharing]
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And the spreadsheetized version: [https://docs.google.com/spreadsheet/ccc?key=0Agy0Ax3YY340dG9PejNPTkZ2Q2RrcjU1WVZMYWxYT2c&usp=drive_web#gid=0]
  
 
== Members ==
 
== Members ==
* Julie Allen
 
 
* Andrea Thomer
 
* Andrea Thomer
 
* Daisie Huang
 
* Daisie Huang
 
* David Eades
 
* David Eades
 +
* Julie Allen

Latest revision as of 10:01, 4 October 2013

What we did: Assessed other taxonomic workbenches, past and present, to try to ID reasons for success/sunsetting, and then glean best practices/things to look out for as a result.

Overall the systems that have been developed seem to fall victim to funding fall-through and shifting of focus and leadership. The systems that have survived seem to be:

  • open source and free
  • developed by or in coordination with practicing taxonomists
  • have steady funding or support (i.e. independent of other grants or projects)
  • are modular and support later changes in design and alteration (Diversity Workbench and Scratchpads in particular)
  • are designed to support collaboration between multiple people (this isn't necessarily something that is required for success, though -- however it's interesting that they seem to be designed for use cases that require collaboration at a distance)
  • seem to be cloud-based, though am unclear on that for a few of them
  • note: couldn’t look at ITIS taxonomic workbench because of gov’t shut down.

Basic best practices and system needs from conversation with Lisa:

  • must provide offline access to data (so entirely cloud based is not great)
  • support rapid data entry (either through import or clear and easy support of transcription)
  • should be able to search from other repositories (GenBank)
  • available on one machine (again, cloud based is not great)
  • must support publication workflow (thus, good reference management modules are important)
  • need to be able to hook into institutional specimen databases (depending on workflow. This means that a workbench either needs to be a solution for tricky institutional database setups (e.g. idiosyncratic DBS or convoluted KE Emu set ups), or something that can work alongside them)
  • for systematists, should fit into existing/common bioinformatics pipelines


Here is our working google doc: [1] And the spreadsheetized version: [2]

Members

  • Andrea Thomer
  • Daisie Huang
  • David Eades
  • Julie Allen