Whitepaper on Open Source Software in Bioinformatics

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• Subject: Whitepaper on Open Source Software in Bioinformatics

• From: Peter Karp <This email address is being protected from spambots. You need JavaScript enabled to view it.>

• Date: Thu, 30 May 2002 09:40:36 -0700

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Whitepaper on Open Source Software in Bioinformatics

Russ Altman, Stanford University

Phil Bourne, University of California, San Diego

Peter D. Karp, SRI International

Teri Klein, Stanford University

Tandy Warnow, The University of Texas at Austin

This whitepaper discusses issues raised by the recent ISCB statement on

Open Source software in bioinformatics (see URL

http://www.iscb.org/pr.shtml), which we strongly support.  Our intent

is to examine the complicated issues behind open-source software in

more depth.

We strongly endorse the notion that bioinformatics software

produced by academic researchers should be available to academic,

government, and commercial users in the bioinformatics and genomics

communitities.  The community must establish certain minimal

conditions of availability to ensure that the results of publicly

funded research projects are available to both the academic research

community and the commercial sector, to ensure that bioinformatics

software can be scientifically validated, and to reduce confusion in

the availability conditions of different software tools.

However, it is important to recognize that there may be legitimate

reasons for using any of a variety of licenses that satisfy the above

requirements.  There is no definitive evidence that any of the

open-source models are either superior (or inferior) to the

alternatives.  Therefore, we oppose a REQUIREMENT for open-source

software.  Let us be clear that we are not against the use of

open-source software models, which have proved useful in many cases:

we oppose a blanket requirement for open-source models.

The essence of this statement is freedom of choice --- we support the

rights of individual reseachers and their institutions to decide the

most appropriate means by which they wish to distribute software they

have generated using grant funds.

1. Ambiguity of the Term "Open Source"

The majority of open-source software is distributed under some form of

open-source license agreement.  Many different license agreements are

used by different entities that distribute what they call open-source

software.

As of January 2002, 30 different open source licenses were endorsed by

the open source initiative

(http://www.opensource.org/licenses/index.html), each of which has

different terms and implications for protection of intellectual

property and commercialization.  This organization is likely to

endorse additional licenses in the future, and other organizations use

still other license agreements that they label as "open source."

The exact terms of these licenses vary considerably.  Some involve

fees for use.  Some prohibit redistribution of the software by anyone

except the software author.  These variations in license terms have

great implications for the user community.

Therefore, the phrase "open source" has come to be virtually

meaningless, and we henceforth use the term in quotation marks to

highlight its ambiguity.  The important question is: what are the

terms of the license agreement that will be used to implement the

open-source concept?

2. Open Source is Not a Silver Bullet

The intent of this statement is not to promote the philosophy that

"open source" is a bad idea, or that "open source" has no merit.

Rather, its intent is to counter the "open source" dogma that "open

source" is a silver bullet that will miraculously cure most of the

difficulties of software development.  Although "open source" does

have advantages in some cases, those advantages have in many cases

been over-stated by the proponents of "open source," in a manner that

ignores many of the complexities of software development.

3. Funding Agencies Should not Require "Open-Source" Software

Funding agencies should literally not require "open-source software"

availability on the part of their grantees because of the ambiguity of

the term.  Furthermore, funding agencies should not require any

particular "open-source" model.  None of its variations are right for

every software project, every scientist, or every institution.

In the majority of cases, the author of a software package and the

author's institution should be free to determine the terms under which

it will be distributed.  Small software packages, or packages that

lack particularly sophisticated algorithms, will probably have little

commercial value.  In these cases, some "open-source" model may well

be the best choice.  An "open-source" model may also be appropriate

for very large software-development projects that span many

institutions, where defining clear intellectual property rights can

become unreasonably complex.

Generally, requirements on distribution licenses for software

developed with support from government funds should be determined

through negotiations between the government and the institution

receiving the support, in concert with existing laws and regulations.

Only in rare circumstances, when the licensing terms are clearly

relevant to the scientific merit of a proposal, should software

licensing terms be considered as part of the peer review process.

The remainder of this section explores different properties of the

"open-source" model.

4. No Fee, Unlimited Redistribution Variation of Open Source

In this variation of "open source," a software package is supplied to

all users for no fee, and no restrictions are placed on the ability of

end users to redistribute the software.

Funding agencies that require bioinformatics software to be

distributed for no fee to all organizations, or that require that

software users must be allowed to redistribute the software source

code, will encourage bioinformatics software tools to become "wards of

the state."  Government funding agencies have limited research budgets

that cannot fund the full costs of every worthwhile project.  It is

advantageous to the government for some bioinformatics software

packages to be commercialized so that the costs of their further

support and development are no longer born by the government, thus

freeing government funds for other new projects.  (We note that

commercialization is also not a panacea, and that not all

commercialization efforts succeed.)

Companies commercialize software largely because they see a

potential financial reward.  Financial rewards usually depend on the

existence of a significant competitive advantage.  A company is

unlikely to commercialize a software package if potential customers

can obtain the software for free elsewhere, or if a competitor has

free access to the complete source code of that package, giving the

original company little advantage over its competitors.  Other

licensing mechanisms exclude competitors, and protect the competitive

advantage that allows companies to make significant additional

investments in the development of a software package.

If commercial entities are unwilling to take over support and

development of key bioinformatics packages, those packages will become

forever dependent on support by the government, thus decreasing the

funds available for other research projects.

Furthermore, government funding is well known to lack long-term

stability, particularly in young interdisciplinary fields such as

bioinformatics, where reviewing quality is highly variable.

Commercial licensing programs can aid a research group by providing an

alternate revenue stream that can supplement, and buffer gaps, in

government funding.  Consider the case of the highly regarded

Swiss-Prot database, which lost its funding from the Swiss government

in 1996.  The Swiss-Prot project adopted a commercial licensing model

that saved this valuable scientific resource from collapse.

Requiring no-fee or unlimited redistribution conflicts with the US

Bayh-Dole act.  It specifies that recipients of US government-funded

research are the owners of copyrightable works (such as software) that

they author.  The author of a copyrightable work may choose the

license under which that work is distributed.  The Bayh-Dole act was

enacted precisely because its authors recognized that commercial

development of research ideas requires just the sort of competitive

advantage just described.  A blanket "open-source" requirement will in

some cases conflict with the individual licensing rules of academic

institutions, putting investigators in the position of mediating

internal legal disputes in order to apply for funding.

Requiring grantees to distribute their software using a no-fee and

unlimited redistribution license would deprive those grantees of the

majority of the potential for being rewarded for their hard work and

ingenuity.  This approach could open the door for commercial

organizations to obtain ma software package, improve upon it, and

then redistribute the package commercially, thus cashing in on the

hard work of the original author with no benefit to that author.

5.  What are the Benefits of Source-Code Availability?

We know of no empirical evidence (such as a scientific study of

software engineering practices) that software projects using an

"open-source" model have a significantly higher probability of success

than projects that distribute software under more restrictive terms

(all other things being equal).  Many successful bioinformatics

software tools are made available under licenses that do not include

source code, such as WU-Blast, Phred, Phrap, and EcoCyc.

Although source-code availability can allow users of a software

package to fix bugs in the software or tailor the software to their

own needs, it is worth noting that for a software package of any

significant complexity, many users will be unable to understand the

source code sufficiently well to fix it or customize it.  Attempted

fixes often introduce new bugs, and it is takes times for the original

authors to test those fixes and re-integrate them into the original

package.

The ability of users to redistribute modified versions of a software

package can lead to the proliferation of multiple incompatible

versions of the software, and to versions that have more bugs than

the original package, thus damaging the reputation of the original

package.

Does source-code availability allow better scientific validation of a

software package?  We know of no examples where inspection of the

source code of a software package revealed fundamental scientific

errors (as opposed to implementation bugs in an otherwise valid

method) that were not detected by the reviewers of associated

publications.  For the purpose of promoting rigorous scientific

evaluation, source code availability is no substitute for a clear

written presentation of an algorithm.  It is typically easier to

validate a program by running it on test cases (which does not require

source code) than by inspecting the source code.

6. Summary

In closing, we do not oppose software licensing in which source code

is made openly available -- we opposes a blanket requirement of

"open-source software."  Many successful existing bioinformatics

software packages have not been distributed using some variation of

"open-source" license agreements.  Licensing arrangements should be

determined by the software authors on a case-by-case basis.  We

oppose government-funded bioinformatics software efforts that do not

make their software available, under some form of license agreement,

to academic, government, and commercial organizations.