This page describes how users, developers, and software become a part of GMOD.
To become a GMOD user, just download, install, and start using one or more GMOD Components. That’s it. There is no mandatory registration process, and you don’t have to meet any set of requirements. GMOD is open to everyone.
You are encouraged to sign up to the (low-volume) GMOD Announce mailing list, and to the mailing list(s) for the components that you use. You can also subscribe to the GMOD News RSS feed. These will help keep you up to date on both the project and the components you use.
Developers are users who also contribute code back to the project. In the early days of GMOD every user was also a developer. This is no longer true, but every user can still become a developer.
There are several ways to become a developer:
Developers are also encouraged to sign up for the GMOD Developer mailing list (and maybe GMOD Architecture as well).
New software components become a part of GMOD through a nomination and evaluation process.
Software can be nominated by its developers, by GMOD users, or by GMOD staff. New components also arise from within the community. Bio%253A%253AChado%253A%253ASchema, DIYA, and MAKER are all recent examples of software becoming a part of GMOD.
Please contact the GMOD Help Desk if you would like to nominate a new component. You can also nominate a component by posting to the GMOD Mailing Lists that are most relevant to the tool.
Nominated software is first evaluated by GMOD staff (currently the GMOD Project Coordinator and the GMOD Help Desk) to see if it meets basic requirements such as open source licensing and GMOD interoperability. We’ll also confirm a good faith commitment of support on the part of the component’s developers. GMOD community members are then asked for feedback on the other requirements such as meeting a common need and useful over time. Community members are picked based on a known interest in the area the new tool addresses. If appropriate, a whole mailing list will be asked to evaluate the software.
GMOD staff will then make a decision based on community input and responses from the developers. The decision may be to include the software, to not include the software, or to include the software after additional development or documentation is done.
To become a part of the GMOD suite, software has to meet several requirements:
Meets a Common Need
First, the program must meet a common need in biological research. A
tool that is only useful with organisms that are two-dimensional (think
butterfly wings), is probably not a good match for GMOD. Tools must be
useful across a wide range of biology, and meet a widespread need. Tools
that support next generation sequencing, gene
expression,
phenotypes, or comparative
genomics are good examples
of broadly applicable tools.
Useful Over Time
GMOD Components should be applicable and useful for at least several
years. For example, GMOD tends to avoid analysis tools because this
area of bioinformatics is constantly changing. However, the need to
connect different analysis tools into reusable pipelines (see
Ergatis and
Galaxy for examples), is a common and longstanding
need that will outlive any particular too.
Configurable and Extensible
GMOD tools should be usable in a wide variety of situations. Different
user environments will require different configurations of the software.
GMOD components should make it easy for users to do this tailoring in
configuration files - they should generally not have to change the
source code itself to get what they want. Another (complementary) way to
achieve this is to have an extensible architecture where computer-savvy
users can write plugins/extensions for tasks such as input/output using
custom/local data sources and formats.
Open Source License for All Users
New GMOD software must have an
Open Source Initiative (OSI) approved license, and
that license must be free to all users. The GMOD project is committed to
open source principles.
Interoperable With Other GMOD Components
New GMOD software must be interoperable with other GMOD
Components. Usually this means that
the software can export and/or import GFF, or that it can
connect to Chado.
Commitment of Support
The developers of the software must be willing to make a good faith
commitment to support the new component for at least 2 years after
joining GMOD. This commitment includes setting up email lists,
responding to user questions, writing and maintaining documentation, and
adding new features and bug fixes to the code.
The current developers should also be open to new developers from the GMOD community contributing code and other support to the new component. This open development model contributes to the long-term viability of the open source model.
Users and Support Mailing List(s)
Newly added software components must have user/support mailing
list(s) and those lists must
be publicly archived.
Public repository
The software component, including code, documentation and other
supporting files need to be stored in a publicly accessible code
repository. This repository must also enable the addition of new
developers over the life of the project.
Being officially part of GMOD has several advantages:
However, a component does not need to be officially part of GMOD to have a presence in GMOD. Any software that is useful to the GMOD community is of interest. See External for a list of such software that currently has a page on the GMOD web site. GMOD is particularly interested in tools (such as Artemis) that interoperate with GMOD components. You don’t even have to apply for GMOD membership to have an “external” page.
These Software Membership Requirements change over time.
| Version | Start | End | Comments | |—-|—-|—-|—-| | 2.0 | December 2010 | - | Added publicly archived mailing list, and publicly accessible source code archive requirements. These revisions were discussed at the September 2010 GMOD Meeting, and on the GMOD Mailing Lists in December 2010. The proposed changes were favorably received at the meeting and on the mailing lists. The Version 2.0 membership standard became official on 2010/12/21. | | 1.0 | February 2010 | December 2010 | Formalized the nomination process and the previously informal membership requirements. | | Informal | Conception | February 2010 | The list of requirements evolved and grew over time, eventually resulting in Version 1. |