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Open-source code

A resource for users or producers of open-source code or software for researchers in biomedical or life sciences

Defining open source

What is open-source software?

Open-source software (OSS) has been defined in numerous ways. Briefly, open-source software is available as source code, without cost, and can be used, modified, and redistributed by others without needing to obtain permissions.

The commonly-accepted - and most complete - definition of open-source software comes from the Open Software Initiative (OSI), listing 10 criteria with which open-source software must comply. This definition, last modified in 2007, was derived from the Debien Free Software Guidelines (DFSG).

The Open Software Initiative's Frequently Asked Questions are a great place to begin learning more about open source software. For an historical perspective, read Christine Peterson's 'How I coined the term "open source"'

What is is open source code?

Open-source code is open-source source code. As with open-source software, open-source code is freely available for use, reuse, and distribution without obtaining permissions. 

Aren't these just two ways of saying the same thing?

Not really. Open-source software is a compilation of open-source code. Open-source code, uncompiled into a software program, can still be useful for developers or users looking for a headstart on developing a script or software program to ask or answer questions, automate processes, or complete tasks.

How can open source software or code benefit me?

If you're a developer:

Develop and share your own open source code, or contribute to an existing project. You can gain experience, help solve interesting problems, get and receive help, and build a profile demonstrating your skills and expertise. Contributing to the open source community is also a great way to advance your projects, as others may jump in to note bugs or fix bugs, write documentation, etc.

Want to learn more, or ready to get started? Github's Open Source Guides are a great place to begin; also check out Github's How to contribute to open source

If you're an end-user:

Use available open source code or software for your data collection, cleaning, analysis or visualization. Share links to the code/software along with your data to make your entire scientific process more open, transparent, and reproducible. 

 

Open Source Initiative definition

From: The Open Source Definition

Open source doesn't just mean access to the source code. The distribution terms of open-source software must comply with the following criteria:

1. Free Redistribution: The license shall not restrict any party from selling or giving away the software as a component of an aggregate software distribution containing programs from several different sources. The license shall not require a royalty or other fee for such sale.

2. Source Code: The program must include source code, and must allow distribution in source code as well as compiled form. Where some form of a product is not distributed with source code, there must be a well-publicized means of obtaining the source code for no more than a reasonable reproduction cost, preferably downloading via the Internet without charge. The source code must be the preferred form in which a programmer would modify the program. Deliberately obfuscated source code is not allowed. Intermediate forms such as the output of a preprocessor or translator are not allowed.

3. Derived Works: The license must allow modifications and derived works, and must allow them to be distributed under the same terms as the license of the original software.

4. Integrity of The Author's Source Code: The license may restrict source-code from being distributed in modified form only if the license allows the distribution of "patch files" with the source code for the purpose of modifying the program at build time. The license must explicitly permit distribution of software built from modified source code. The license may require derived works to carry a different name or version number from the original software.

5. No Discrimination Against Persons or Groups: The license must not discriminate against any person or group of persons.

6. No Discrimination Against Fields of Endeavor: The license must not restrict anyone from making use of the program in a specific field of endeavor. For example, it may not restrict the program from being used in a business, or from being used for genetic research.

7. Distribution of License: The rights attached to the program must apply to all to whom the program is redistributed without the need for execution of an additional license by those parties.

8. License Must Not Be Specific to a Product: The rights attached to the program must not depend on the program's being part of a particular software distribution. If the program is extracted from that distribution and used or distributed within the terms of the program's license, all parties to whom the program is redistributed should have the same rights as those that are granted in conjunction with the original software distribution.

9. License Must Not Restrict Other Software: The license must not place restrictions on other software that is distributed along with the licensed software. For example, the license must not insist that all other programs distributed on the same medium must be open-source software.

10. License Must Be Technology-Neutral: No provision of the license may be predicated on any individual technology or style of interface.