Difference between revisions of "Student Instructions"

From phenoscape
 
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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]].
  
===2. Create a SourceForge account===
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===2. Use DropBox to work with project files ===
We use [http://sourceforge.net/ SourceForge] to maintain our data files and you'll need a username and password to work with these files.
 
  
===3. Use DropBox 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.
  
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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===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.
  
===4. Download PDFs from the Phenoscape Fileshare ===
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Note: PDFs for teleost publications are housed on a file share; see access instructions below:
Download publication PDFs by connecting to the Phenoscape file share.  Please ask a Phenoscaper for the username and password.
 
  
 
====Mac OS X====
 
====Mac OS X====
 
# In finder > Go > Connect to Server
 
# In finder > Go > Connect to Server
 
# Type in
 
# Type in
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<nowiki>https://webdav.nescent.org/phenoscape-data</nowiki>  
 
<nowiki>https://webdav.nescent.org/phenoscape-data</nowiki>  
 
# Accept security warning about certificate
 
# Accept security warning about certificate
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# Click Next twice
 
# Click Next twice
 
# In internet or Network address box, type in
 
# In internet or Network address box, type in
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 +
 
<nowiki>https://webdav.nescent.org/phenoscape-data</nowiki>  
 
<nowiki>https://webdav.nescent.org/phenoscape-data</nowiki>  
 
# Accept certificate warning, if given.
 
# Accept certificate warning, if given.
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# Finish
 
# Finish
  
===5. Subscribe to Curator Mailing List ===
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===4. Subscribe to Curator Mailing List ===
 
* Phenoscape Curators mailing list (for discussion and communication of data curation issues, solutions, and progress):  http://lists.sourceforge.net/lists/listinfo/phenoscape-curators
 
* Phenoscape Curators mailing list (for discussion and communication of data curation issues, solutions, and progress):  http://lists.sourceforge.net/lists/listinfo/phenoscape-curators
  
===6. Create Tree Files ===
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===5. Create Tree Files ===
  
 
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.]]
 
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.