Difference between revisions of "Student Instructions"

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Phenex is used by Phenoscape for curation of evolutionary phenotypes.  You can find instructions for downloading and installing Phenex at the [[Phenex|Phenex homepage]].
 
Phenex is used by Phenoscape for curation of evolutionary phenotypes.  You can find instructions for downloading and installing Phenex at the [[Phenex|Phenex homepage]].
  
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===2. Use DropBox to work with project files ===
  
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===2. Using ZigVersion to work with project files ===
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Phenoscape project files are XML files (more specifically, they are in [http://nexml.org NeXML] format) created using Phenex and housed in a shared [http://www.dropbox.com DropBox] folder (named 'Phenoscape-data').  Please contact Wasila or Paula for access.
  
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Phenoscape project files  are housed in a subversion-controlled data repository, and we use [http://sourceforge.net/svn/?group_id=224046/ Subversion] to manage local and repository copies of the files.
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===3. Access PDFs from the Phenoscape Mendeley library ===
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PDFs are shared using Mendeley. Please ask Paula or Wasila for access to the group.
  
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# Download and install [http://zigversion.com/ ZigVersion]. This application is for Macs only. Remember to drag the icon from the installation dialog box to your Applications folder.  Also download the free, non-commercial [http://zigversion.com/ license]. This requires that you provide your name and email address, and the license file is immediately emailed to you.  Don't open this license file, just drag to the License dialog box that appears when you first run ZigVersion.
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Note: PDFs for teleost publications are housed on a file share; see access instructions below:
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# Follow [[Data Repository Access Instructions| this tutorial to learn how to use ZigVersion.]]
 
  
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Once you have obtained the software and files, you can begin working.
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====Mac OS X====
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# In finder > Go > Connect to Server
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# Type in
  
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===== ''Always follow these steps to begin and end your work session:'' =====
 
  
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# Start up ZigVersion and connect to repository
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<nowiki>https://webdav.nescent.org/phenoscape-data</nowiki>
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# Select the top-level folder named with a forward slash (/)
 
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# Click "update" to download recent versions of files to your local, working folder
 
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# Within Phenex, open the local copy of your file and proceed with your curation work.
 
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# After completing work and saving your file, go back to ZigVersion and Check In your modified file(s) to the repository.
 
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## select the file and click “Check In”; you can also check in a batch of modified files by selecting the top level folder
 
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## type in a comment that describes your work on each file (e.g., “added free text character descriptions for 1-100”, “proofread matrix and taxon list”…)
 
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====3. Download PDFs from the Phenoscape Fileshare ====
 
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You can download publication PDFs and powerpoint posters of the TAO and PATO ontologies by connecting to the Phenoscape file share.
 
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Connecting in MAC OS X
 
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# In finder > Go > Connect to Server
 
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# Type in https://ftp.nescent.org/[sharename] .  For example, https://ftp.nescent.org/phenoscape-data
 
 
# Accept security warning about certificate
 
# Accept security warning about certificate
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# enter username and password (ask a Phenoscaper)
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# enter username and password
  
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Connecting in Windows XP
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====Windows XP====
 
# Go to "My Network Places"
 
# Go to "My Network Places"
 
# Add a Network Place (pulls up wizard)
 
# Add a Network Place (pulls up wizard)
 
# Click Next twice
 
# Click Next twice
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# In internet or Network address box, type in https://ftp.nescent.org/phenoscape-data/
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# In internet or Network address box, type in
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**Note:  (there is a bug in MS implementation of webdav client. In fact, Internet explorer and this method use two different means of connecting to webdav. go figure. Therefore, you must suffix the URL with the pound sign as a workaround to the bug.
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<nowiki>https://webdav.nescent.org/phenoscape-data</nowiki>
 
# Accept certificate warning, if given.
 
# Accept certificate warning, if given.
 
# Give the share a meaningful name. Default is usually fine.
 
# Give the share a meaningful name. Default is usually fine.
 
# Finish
 
# Finish
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===4. Subscribe to Curator Mailing List ===
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* Phenoscape Curators mailing list (for discussion and communication of data curation issues, solutions, and progress):  http://lists.sourceforge.net/lists/listinfo/phenoscape-curators
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===5. Create Tree Files ===
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We use [http://mesquiteproject.org/mesquite/mesquite.html Mesquite] to create nexus files containing trees replicated from fish publications.  See this page for [[Creating_Tree_Files|instructions on creating tree files using Mesquite.]]
  
 
[[Category:Curation]]
 
[[Category:Curation]]

Latest revision as of 20:06, 29 November 2012

1. Download Most Recent Version of Phenex

Phenex is used by Phenoscape for curation of evolutionary phenotypes. You can find instructions for downloading and installing Phenex at the Phenex homepage.

2. Use DropBox to work with project files

Phenoscape project files are XML files (more specifically, they are in NeXML format) created using Phenex and housed in a shared DropBox folder (named 'Phenoscape-data'). Please contact Wasila or Paula for access.

3. Access PDFs from the Phenoscape Mendeley library

PDFs are shared using Mendeley. Please ask Paula or Wasila for access to the group.

Note: PDFs for teleost publications are housed on a file share; see access instructions below:

Mac OS X

  1. In finder > Go > Connect to Server
  2. Type in


https://webdav.nescent.org/phenoscape-data

  1. Accept security warning about certificate
  2. enter username and password

Windows XP

  1. Go to "My Network Places"
  2. Add a Network Place (pulls up wizard)
  3. Click Next twice
  4. In internet or Network address box, type in


https://webdav.nescent.org/phenoscape-data

  1. Accept certificate warning, if given.
  2. Give the share a meaningful name. Default is usually fine.
  3. Finish

4. Subscribe to Curator Mailing List

5. Create Tree Files

We use Mesquite to create nexus files containing trees replicated from fish publications. See this page for instructions on creating tree files using Mesquite.

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