Phylemon: A common environment

If you have created an account and get logged in following the instruction in the My first project section, you should see on the top right part of the page your user email and the project you are working in (active). At the same level, on this gray bar, you should find:

• information about the number of active jobs you have
• the space you have used over your 1 GigaByte account
• link to the data you have uploaded/generated in Phylemon
• link to your projects and their jobs
• link to you account characteristics
• logout to logout

The icons on the right side

All this fields are visible from every location inside Phylemon (while you are logged in)

The left side bar is a new feature in Phylemon2 that lets users have a quick view on the last run jobs and uploaded data (all information contained in the side bar is accessible via the project management and data management ).

“Job list” view	“Data list” view	Collapsed view (only “summary view”)

• Switching between the “Job list” view and the “Data list” view can be done by clicking on them.
• Under the Job list view extra features are available to select a specific set of jobs:
  • only jobs corresponding to current project
  • back to all jobs
  • only running jobs
• Summary field: The side bar can be collapsed or expanded by clicking on its gray bar on the left (summary field):
  • it contains different spots to summarize the activity of your jobs (the number in white next to the spot stands for the number of corresponding jobs):
    • number of finished and unvisited jobs
    • number of visited jobs
    • number of running jobs
    • number of jobs waiting to be run
  • Some other icons may appear:
    • when a new job is finished
    • when a new data is generated

In order to ease data manipulation user can access to all files uploaded or generated in the data section . In the Data section user will find all his files in two sections “uploaded data” and “Data by job”.

Each data file is labeled, either by the user if it has been uploaded, or by Phylemon if the file has been generated by a tool. The labels are necessary to smooth redirections and also to ease the selection of the files when picked from the server (see example bellow for Muscle), as each input field in any tool or utility will be looking for specific labels, files that do not correspond will appear in gray. Labels available in Phylemon are:

• Aligned sequences
• Non-aligned sequences
• Distance matrix
• Tree
• Weights
• Pipeline
• Compressed

Each one of the tool hosted by Phylemon is fitted in a specific environment with common fields letting you to get used to it.

• The Help link directly send users to the software page.
• The Citation link show the bibliographical reference(s) corresponding to the current tool (if published).
• Online examples: each one of the tool and utility in Phylemon is served with at least one example that can be loaded at the same time as the parameters best fitting with the example.
• Project management: you can fill the Job name and Job description fields, to ease organization.
• Most of the outputs of each tools/utility can be redirect to other tools/utilities.

Each one of this points is illustrated in the Trial on MyFirstProject section