Difference between revisions of "Student Instructions"

From phenoscape
(4. Create Tree Files)
(4. Create Tree Files)
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===4. Create Tree Files ===
===4. Create Tree Files ===
We use [http://mesquiteproject.org/mesquite/mesquite.html Mesquite] to create nexus files containing trees replicated from fish publications.  You should have a [http://sourceforge.net/ SourceForge] account and access to the [[Data_Repository_Access_Instructions|Phenoscape Data Repository]] before beginning.
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.]]

Revision as of 21:52, 10 February 2009

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 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”…)

3. Download PDFs from the Phenoscape Fileshare

You can download publication PDFs by connecting to the Phenoscape file share.

Connecting in MAC OS X

  1. In finder > Go > Connect to Server
  2. Type in https://ftp.nescent.org/[sharename] . For example, https://ftp.nescent.org/phenoscape-data
  3. Accept security warning about certificate
  4. enter username and password (ask a Phenoscaper)

For Windows XP users, see instructions here

4. 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.