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. | + | ===2. Use DropBox to work with project files === |
| − | |||
| − | + | 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 | + | ===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==== | ====Mac OS X==== | ||
# In finder > Go > Connect to Server | # In finder > Go > Connect to Server | ||
# Type in | # Type in | ||
| + | |||
| + | |||
<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 | ||
| Line 25: | Line 26: | ||
# Click Next twice | # Click Next twice | ||
# In internet or Network address box, type in | # In internet or Network address box, type in | ||
| + | |||
| + | |||
<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 | ||
| − | === | + | ===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 | ||
| − | === | + | ===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
Contents
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
- In finder > Go > Connect to Server
- Type in
https://webdav.nescent.org/phenoscape-data
- Accept security warning about certificate
- enter username and password
Windows XP
- Go to "My Network Places"
- Add a Network Place (pulls up wizard)
- Click Next twice
- In internet or Network address box, type in
https://webdav.nescent.org/phenoscape-data
- Accept certificate warning, if given.
- Give the share a meaningful name. Default is usually fine.
- Finish
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
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.
