Student Instructions

From phenoscape
Revision as of 15:45, 9 April 2009 by Wasila (talk | contribs) (4. Download PDFs from the Phenoscape Fileshare)

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. Create a SourceForge account

We use SourceForge to maintain our data files and you'll need a username and password to work with these files.

3. Use ZigVersion to work with project files

Phenoscape project files are housed in a subversion-controlled data repository, and we use Subversion to manage local and repository copies of the files.

  1. Download and install 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 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.
  2. Follow this tutorial to learn how to use ZigVersion.

Once you have obtained the software and files, you can begin work.

Always follow these steps to begin and end your work session:
  1. Start up ZigVersion and connect to repository
  2. Select the top-level folder named with a forward slash (/)
  3. Click "update" to download recent versions of files to your local, working folder
  4. Within Phenex, open the local copy of your file and proceed with your curation work.
  5. After completing work and saving your file, go back to ZigVersion and Check In your modified file(s) to the repository.
    1. select the file and click “Check In”; you can also check in a batch of modified files by selecting the top level folder
    2. 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”…)

4. Download PDFs from the Phenoscape Fileshare

Download publication PDFs by connecting to the Phenoscape file share. Please ask a Phenoscaper for the username and password.

Mac OS X

  1. In finder > Go > Connect to Server
  2. Type in
  3. Accept security warning about certificate
  4. 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
  5. Accept certificate warning, if given.
  6. Give the share a meaningful name. Default is usually fine.
  7. Finish

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.