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SBML Projects

This is the top-level page for projects being worked on by the SBML Team. This page summarizes the tools we use and how we organize the work, while subpages deal with specific project details.

Overall approach

We keep a spreadsheet in Google docs listing the team personnel and their general involvements and responsibilities. (This spreadsheet is private to the team.) This responsibilities matrix is not fixed in stone; people's involvements change over time, pretty much on an as-desired basis. In general the goal is to keep people working on things that interest them and keep them motivated, with an eye to trending towards completion of the goals given in the NIH grant funding the work on SBML.

Our set of software tools for project management, communication, and general organization consists of the following.

  • The wiki (i.e., this site) for storing information and organizing projects overall
  • SourceForge for SVN and file distribution
  • Pivotal Tracker for project management
  • Twitter feed "sbmlprojectfeed" for project updates
  • GNU Mailman for mailing list management, using lists hosted at and (depending on the list)
  • Skype for teleconferences and chats
  • SurveyMonkey for community surveys
  • A.nnotate for sharing annotated web pages, PDFs, and more
  • Email for general communication

The following subsections contain notes for SBML Team-specific configuration and use of some of these tools.

SVN on SourceForge

The SBML Team's official public code repository is on SourceForge. Access, configuration and use of our SVN repository is described on a separate page.

Pivotal Tracker

When creating a new project, some of the default configuration values in Pivotal Tracker (abbreviated as "PT" in the rest of this text) are worth changing slightly to better suit our style of work. Here is a step-by-step procedure for how Mike creates new projects in PT:

  1. Go to your PT dashboard
  2. Click on the Create Project + button next to My Projects
  3. Give the project a title and press return
  4. PT generates the project and puts you into the story page. There is a series of dark blue buttons above the large blank areas. Click on the View button, thereby making a drop-down menu appear, and from this, select the option Settings. (See the screenshot.)
  5. In the Settings page that comes up, change the values as follows:
    1. Point Scale: change to "Custom" and use the following: 0, 1, 2, 4, 8, 16, 40
      Meaning of points: our points correspond roughly to hours. The value "0" represents a short task that is estimated to take less than one hour of time. This is not strictly how points are meant to be used in Pivotal Tracker, but this has worked best for us. The exponential scale captures the increasing amount of uncertainty that accompanies any attempt to guess how long a large task will take—we're generally better at guessing accurately how long a 2-hour task will take than a 16-hour long task.
    2. Initial velocity: set to 2
    3. Enable RSS/Atom: click to enable
    4. Enable Tasks: click to enable
    5. Bugs and Chores May Be Given Points: click to enable (yes, despite that it's discouraged)
    6. Click the Save Settings button at the bottom. Ignore the warning about having changed the point scale.
  6. Next, click on the Members tab, and add everyone in the team as an Owner (note: not merely a Member)
  7. Next, click on the Project profile tab, and add a description for the project
  8. Finally, click on the Integrations tab, and enable the Twitter feed integration for sbmlprojectfeed

When a project is completed, archive it to remove it from the list of active projects. To do this, go back to the Settings area for the project, click on the Overview tab, and look for the item Archive in the Actions subsection.

On a separate page, we keep a list of general procedures that we try to follow in our use of Pivotal.

"sbmlprojectfeed" Twitter feed

Pivotal Tracker provides a facility for creating Twitter feeds for every project. We have a Twitter user called sbmlprojectfeed for the purpose of aggregating all project news into a single feed. By turning on Twitter integration for every PT project we create, and setting the Twitter destination to be sbmlprojectfeed, every action on a project in PT will automatically cause a tweet to be generated. Anyone who's interested can subscribe to this Twitter feed to see what's happening in the SBML projects.

Mailing list management via Mailman

The mailing lists and our general procedures for their management are described on a separate page.

Software release procedures

The steps we follow to update different software packages are detailed on separate pages associated with the software packages in question. A listing is provided on a separate page.

Document release and update procedures

Documents such as the SBML specifications are hosted on the website. The SBML Team maintains them according to schemes described on a separate page.

SurveyMonkey for surveys

We have a paid account with SurveyMonkey for running community surveys. We found a way to embed the surveys directly in We provide some notes on a separate page about how we configure our SurveyMonkey surveys.

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This page was last modified 19:57, 6 October 2013.

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