Welcome to the ISCB Community News Blog

This blog collects news, announcements or other information which could be of interest to our ISCB members. We are a group ISCB members who volunteer to populate this blog on a regular basis. In case you want to become an "ISCB-News Reporter" yourself, let us know: contact ISCB
Don't repost copyrighted content! The guidelines are:
- Include a link to the source page
- Include a short summary about the article. You can quote up to ONE paragraph from the original story, but not more
- Don't repost an entire articles originating from another source
- Never post content without attribution — always include the source

To post a news, please use this form.

Monday, May 10, 2010

ISCB Member Feedback Sought on (Draft) Literature Open Public Access Policy Statement

International Society for Computational Biology
ISCB (Draft) Literature Open Public Access Policy Statement
Draft approved by the ISCB board of Directors on April 8, 2010

Open for comment from the ISCB membership
and bioinformatics community

Comment period closes June 11, 2010

The International Society for Computational Biology (ISCB) is dedicated to advancing human knowledge at the intersection of computation and life sciences. This (draft) ISCB policy statement is intended to express strong support for open public access to the archival scientific and technical literature and to elucidate in more nuanced detail the position of ISCB on this important issue in scientific publication.

An official ISCB policy statement on the closely related topic of sharing software provides very clear support for Open Source/Open Access (http://www.iscb.org/iscb-policy-statements-/187). ISCB supports many of the principles of the “Budapest Open Access Initiative,” the “Bethesda Declaration on Open Access Publishing,” the U.S. National Academies of Sciences report on "Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences," and the European “Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities.”

Knowledge is the fruit of the scientific research endeavor, and the archival scientific literature is its practical expression and means of communication. Shared knowledge multiplies its utility because every new scientific discovery is built upon previous scientific knowledge. Access to knowledge is the power to solve new problems and make informed decisions. More open public access to archival scientific and technical knowledge will empower more citizens and more scientists to solve more problems and make more informed decisions.

    1. There should be free, open, online, public access to research results in the archival scientific and technical literature, with all their existing content including supplementary material and data. This access may be at an interval following publication, which interval should not exceed one year.

    2. Existing models show high impact, scientific benefit, feasibility, and acceptability:

      a. The public benefit from open access to the world’s online information via the publicly-funded Internet provides a good model of expected impact.

      b. The scientific fertilization from open access to genomic information via the publicly-funded Human Genome Project provides a good model of expected scientific benefit.

      c. Open access policies by the U.S. National Institutes of Health, the Howard Hughes Medical Institute, and the Wellcome Trust provide good models of feasibility, acceptability, and implementation.

    3. Open literature access will enable a whole new generation of innovative tools and mechanisms that will endow the literature with enriched commentary and usability and connect the literature and databases via the proper pointers. These tools are already being built by publishers, researchers, and others. The creation of the web of knowledge around publications is an important consequence of semantic enrichment of the literature.

    4. Whether publications are immediately available or delayed, the underlying data and methods must be publicly available in sufficient detail to allow replication of the results and application of other computational methods to the data.

    5. Policy details — which version, where stored, how annotated and organized, what incentives — must be considered carefully. However, it has become essential to put forward a broad policy mandate for eventual public access to research knowledge.

    6. Publishing high-quality peer-reviewed scientific literature incurs costs. We recognize that cost recovery is a serious issue that must be addressed carefully if open access is to be a mandated policy.

    7. The funding policy must:

      a. Fund activities of peer review, copy editing, and publishing.

      b. Provide fair compensation, if and where needed, to facilitate transitions and adaptations to new models for publishing and sustaining essential revenue.

      c. Be consistent with government laws, other existing regulations, and research dissemination through viable commercial mechanisms.

    8. It is undesirable to take funding from current research and thereby risk underfunding basic science, so new funding should be made available for policy implementation. However, the expected total cost for complete open literature access is only a very small percentage of the total cost for the entire international research endeavor.
Scientific literature represents a substantial investment by governments, foundations, and others. One of our primary missions is the assembly of individual pieces of knowledge from this literature in ways that provide powerful new insights and ideas for next-stage research by the entire scientific community and society in general. We in the ISCB are committed to the continuous enhancement and leveraging of mankind’s knowledge resources. To achieve this goal, investment in open public access to the research literature must be made.

ISCB (Draft) Literature Open Public Access --- Appendix

A. Documents mentioned in the statement text.
1. Text of the “Budapest Open Access Initiative.”

2. Text of the “Bethesda Declaration on Open Access Publishing.”

3. Text of the U.S. National Academies of Sciences report on "Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences."

4. Text of the “Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities.”

5. Text of Open Access Policy from the U.S. National Institutes of Health.

6. Text of Open Access Policy from the Howard Hughes Medical Institute.

7. Text of the Wellcome Trust's "Position Statement in Support of Open and Unrestricted Access to Published Research."

B. General Background Material.
1. Academic publishing - Wikipedia, the free encyclopedia.

2. Open access (publishing) - Wikipedia, the free encyclopedia.

3. ROARMAP (Registry of Open Access Repository Material Archiving Policies) as recommended by the Berlin Declaration.

C. Other Statements and Materials.
1. Text of Public Library of Science "Open Letter to Scientific Publishers" (signed by ~34,000 scholars worldwide).

2. Text of Research Councils of the UK "Access to Research Outputs."

3. Text of European Research Advisory Board Final Report "Scientific Publication: Policy On Open Access."

4. Text of Bulletin of the World Health Organization "Equitable access to scientific and technical information for health."

5. UNESCO EBSCO Open Science Directory.

6. Peter Suber's "Open Access Overview."


  1. While I am in favor of open access literature, I think that this statement is too weak on how to pay for it. The current author-pays model has the effect of locking unfunded or underfunded researchers out of publication. I believe that a healthy publication community requires a mix of author-pays, reader-pays, and other models for recovering the costs of publication, but this statement comes down too heavily in favor of author-pays.

    Perhaps what we need are some direct federal grants to journals to cover publication costs, so that neither the author nor the reader pays. (Though I can see problems with that as a sole model also.)

  2. I respectfully disagree with Kevin Karplus: the draft statement is entirely and deliberately neutral about choices among author-pays, reader-pays, and other models for recovering the costs of publication. It does not, and cannot, come down in favor of author-pays --- because it does not come down in favor of any particular payment mechanism at all.

    The draft statement is very careful to state as a goal the noble principle of the general good, while being open to the possibility that many different implementations all may achieve that good goal.

    Indeed, the situation is similar to the computer science principle that the system architect should articulate the desired system behavior, while leaving the choice of the most efficient system implementation open, to be decided by the system implementers.

  3. The problem here, then, is incomplete specification. It needs to be explicit that whatever mechanism is created must unduly not favor well-funded over poor funded scientists.

    To continue the CS analogy, it's like a system architect leaving out the requirement of fairness in scheduling.

  4. Hi all,

    Perhaps related to the comments so far, I think a third option which is rarely discussed is a "both-pay" model. That is, if under the author-pays system, authors pay $2000 USD per paper, and under the reader-pay system, they pay some amount that ends up being about the same, why not have a both-pay system where both sides pay $1000 each? While such an approach is difficult to calculate for publishers, it is probably fairer.

    Some institutions might find it difficult to come up with $2000 per paper, but $1000 each might be more feasible and the remaining $1000 can be used on papers they actually read and cite. One problem with an author-pays system is that publishers can lower their standards in order to raise revenue. Contrary to the spirit of this Policy Statement, I think this will hurt science.

    Coming up with prices will be difficult for the average person like myself, but publishing companies surely have paper downloads in one spreadsheet column and author revenues in another and it is a "simple" matter of moving a knob to see where the balance between costs is. Ok...it is not that simple. But, just a suggestion...

  5. Existing "closed" publishing models hamper our ability to even imagine new business models. Commercial competition between "free and open source" software and "proprietary" software has created a vibrant software ecosystem. We can achieve a similar end in academic publishing. To do that, please, consider augmenting recommendation 1 so that it more clearly permits both commercial use and derivative works!

    See: http://en.wikipedia.org/wiki/Libre_knowledge

  6. I believe the statement must include a conflict of interest statement. Any affiliations with a publishing organization would be a conflict for the ISCB and should be clearly stated in this statement. Any other conflicts should also be stated.

    Tom Caruso

  7. For me this statement captures some obvious features of our scientific life. I am encouraged that ISCB leads by example with its own publications, and that it is willing to act as an advocate to others. We can try to anticipate the way $$ and politics might respond to our needs going into the future, but that is not our core competence. It will be interpreted by others as a statement by a scientific community saying what we need to have happen if our labors are to have the impact we can imagine.

  8. There is great value in the open sharing of ideas and data.

    But lost in the idealism is the question: who pays?

    We scientists in Western countries have benefitted tremendously from the generous government funding that has supported sciences for the last 40+ years.

    But if one looks around and observes what is going on, this isn't by any means assured in the future.

    Just today, I saw a chart of debt-to-GDP ratios, and across the developed world the budget situation is bad and growing worse.

    Will societies continue to lavish money on science as the budget noose tightens? I'm not so sure.

    All this Open Access talk depends on a "free and open" funding model.

    For example, if the NIH is funding a researcher like myself, then it is legitimate for them to direct me to be open with the data and results.

    But since ISCB doesn't provide funding (as far as I know), it is more tenuous for the organization to impose a particular view, without the funding that is necessary for that to happen.

    Scientists in the future are likely to need to be more entrepreneurial just to pay the bills. I'm not saying that I agree with it or like it, just that it seems a likely outcome.

    If one has to resort to non-governmental funding sources to do the work, the immediate and open release of data may not be quite so easy, because of the need for IP protection.

    One way that this statement could be modified is to acknowledge the sometimes "need" to protect IP through patenting, with strong encouragement to publish immediately after IP protection is obtained. That is, after all, the reason the patent system exists: to encourage sharing of ideas rather than people keeping those ideas completely closed and proprietary.

    I want to be clear that I'm a supporter of open access. All my lab's software and most of my lab's papers are open access.

    Yet I fear that, by assuming the future is going to look like the past (it almost never does), that we might be implementing something which lacks some foresight about the realities we will all face when funding becomes more limited.

  9. I was not going to comment, but given the above I'd like to register support for the statement as drafted. I agree with Rick that it careful to separate goals and implementation. The most important things in it, in my view, are items 7 and 8. If anything, I think they should be strengthened to take the position that, regardless of the means chosen to achieve it, research funders should bear all costs of dissemination of results.

  10. Is this policy meant to apply to research conducted without public financing? If neither the research nor the journal receives public financing, I think the requirement that access be free within one year is not reasonable.

  11. Lee - the physics community has used the Arxiv.org "preprint" server for many years. Virtually all ISCB articles could be submitted to Arxiv.org Numerous scientists, in other fields, use similar repositories without any need for pay access.

    Can you give a specific example of an article, suited for an ISCB audience, that could not be deposited at Arxiv.org?

    Do journals you use prohibit authors from depositing their articles to a free repository? Examples would really help me (and others) think about this!

  12. AWZ — In Biology, many journals do not have page charges and thus the atmosphere is somewhat different from Physics. For instance, the policy for Oxford Journals, such as Bioinformatics, is posted here; see especially the last five paragraphs. In many cases the policy permits the submission of unrefereed pre-prints to such as Arxiv.org, though only prior to acceptance for publication. Once acceptance is made, no version of the paper may be submitted to a pre-print server, though authors are encouraged to label previously submitted pre-prints with the name of the journal to which they have been accepted. The post-print (after referees, but prior to page proofs) version can be submitted to repositories only if is embargoed for 12 months. And, everything is more permissive if the authors pay the publisher for open access.

    However, that isn't really the point I was trying to make in my previous post. I find the proposed ISCB policy vague as to which research the policy is supposed to cover. Is the policy meant to cover research at a private company that is published in a journal? Is it meant to cover a book of research results that is produced without public financing, e.g., is it meant that Durbin, Eddy, Krogh, & Mitchison (ISBN-13: 978-0521629713) should be available for free after one year?

    Although it may not be the broadest possibility, I am thinking that the safest route is to have the ISCB policy apply only when the research and/or publishing process receives public financing.

  13. It seems to me that, while the idea of public repositories for data and knowledge is widely accepted, the issue is 'Who pays'. However, this is already answered in point 7 which implies that funding research means also funding its dissemination. Indeed, many research budgets include 'cost of dissemination of results' , typically utilized for meetings and travel: it makes perfect sense to include publications costs in the category. Other ways of public funding for research spreading are always welcome.

    The principle is contradicted in point 8, where it says that 'it is undesirable to take funding from current research'. In fact, this is the very point that finds me in disagreement. In publicly funded work, the public should be considered the 'owner' of the research results even before it is made. If the research is 'privately' funded, it is obvious that the funders will use it as they consider best: publication in open format, in 'closed' format, as patent descriptor or in any other fashion.

    A note on the comment by Morgan. Things will probably change, but we don't know how: it might be that people start publishing research, software etc. on their own website, for free, and rely on internet search engines for dissemination. This system might become sophisticated enough to substitute entirely the need for reviewers, editors and publishers.. Again, I'm not saying that this will be the case, or that I wish or like it. Simply: we still don't know.

    Finally, in the Conclusion, I would prefer to see more accent on the public (as the community of scientists and non-scientists) rather than government and foundations (perceived as something 'other than us').

    Also, most likely you mean humankind, not man, yes?

  14. "This is already answered in point 7 which implies that funding research means also funding its dissemination."

    But not all research is funded. Are only funded researchers to be allowed to publish in the new model?

  15. Viewed globally, there are many special-interest constituencies that will be affected one way or another by how the details of open access ultimately work out. Unfunded researchers are one. Researchers from the developing world who have limited funds are another. Professional societies that depend on journal charges for revenue to keep their societies solvent are a third. An instant's thought will reveal several other special-interest constituencies that would be affected, one way or another.

    In all of these cases, the general approach of the proposed statement is to be neutral about these special-interest constituencies, while advancing the broad view that open access is an important idea which should be done now to benefit all of science and technology.

    The general worry is that building into the statement the multiple views of the multiple affected special-interest constituencies would constrain the implementation choices too much, and thus impede the general good.

    It is generally true that "fairness" depends on one's situation, one's viewpoint, and one's context. To attempt to articulate what is and is not “fair” for every situation, viewpoint, and context would result in a bulky and unworkably complex statement.

    Perhaps the most persuasive call for "fairness" comes from the health concerns of the developing world, where literally millions of people will live or die depending on the outcomes of biomedical research.

    I suggest that everyone first read the open access statement by the World Health Organization (WHO), included in the supporting material, part of which is quoted here: "Health is perhaps the area of most intense demand for greater access to scientific and technical information, partly because failure to obtain it can be literally fatal. A public which pays for most medical research through taxes and other public funds is becoming increasingly puzzled by the barriers that deny access to the results of that research. The time is ripe for action."

    The proposed public policy statement by the ISCB calls for action, without specifying an implementation. This course is wholly appropriate for a policy statement.

  16. I would disagree with Kevin when he says that "not all research is funded". Yes, he is correct in that not all research is funded via specific grants, but "unfunded" research is funded by individuals salaries/institutions, or by interested individuals themselves.

    Where an organisation such as a research council or charity funds research, they have every right to want to maximise the impact of such research by having it published in an open access journal. I know that I personally tend to read more papers from journals that are open access and prefer to publish in open access journals.

    There is plenty in the statement about data access and research results. There is little about algorithm implementations. In a data-rich society, analyses cannot realistically be assessed by reimplementing new algorithms. Some approach must be made to ensure that algorithms published for academic scrutiny are available as implementations that also allow academic scrutiny.

  17. I have no objection to research funders demanding that the research they fund be made open-access---indeed I think it is an excellent idea.

    I do object somewhat to the idea that independent scientists are not allowed to publish unless they pay or get someone else to pay for their publication up front.
    Or that universities be required to pay for their faculty's publications (though that might be cheaper than the current model where the universities have to pay for what their students and faculty might read).

    I'm also worried because the average quality of open-access publications seems to be much lower than the average quality of subscriber-journal publications. The business model for open-access encourages making the filter as loose as possible (so that almost any sort of crap gets published), while the business model for subscriber-pays journals requires a fairly tight filter (since the subscribers won't pay for lots of crap). I think that a healthy publishing environment requires both highly selective and rather unselective journals.

    I disagree with the statement "The proposed public policy statement by the ISCB calls for action, without specifying an implementation. This course is wholly appropriate for a policy statement."
    It is inappropriate to issue policy statements without considering the consequences. When some implementations of the policy can clearly have bad consequences, it is at least necessary to discuss the risks to the policy and not pretend that there are none.

  18. As a member of ISCB and on behalf of the MGED Society, I want to express our strong support for the open access policy statement. Requirement of deposition in appropriate public repositories should be explicitly stated for effective open public access to archival scientific and technical knowledge (recommendation 1). Sufficient detail to allow replication of the results and application of other computational methods to the data (recommendation 4) requires following established standards. The seminal MIAME requirements have inspired many similar lists (see http://mibbi.org) including one addressing high throughput sequencing (MINSEQE). Data deposition is free of charge and open source software is available to facilitate this process for 'omics-related data (e.g. http://code.google.com/p/annotare/ ). The MGED Society believes that data deposition is an essential part of publishing an 'omics experiment and has created resources to assist investigators in this work ( http://shareyourdata.org ).

  19. The ordinary courses are additionally pricey and this may be a hindrance for understudies wishing to seek after a MBA yet can't bear the cost of the costly universities. Symbiosis Distance mba