This page has instructions to authors for the Bioinformatics Journal
Instructions[]
Before you submit your article you should think about copyright and copyleft. Copyright is concerned with intellectual property. Copyright law protects a particular form in which ideas are presented by an author. Copyright is not designed to protect the actual concepts and ideas present in your article. If you want to protect the form of your article from being freely copied and distributed, do NOT add your article to this wiki (academia.wikicities.com). If you want to protect the form of your article from being freely copied and distributed you should publish it in a "fixed medium" such as in a printed journal or on a CD-ROM.
Bioinformatics Journal is committed to the idea that the fruits of intellectual activity should be widely distributed, without the restrictions to distribution that can be imposed by copyright. In particular, if you publish your article in Bioinformatics Journal, you explicitly give up your right to have control over the production of copies of your article and you give up your control over the right of others to create derivative works. However, all copies of your article must give credit to you, the author, and derivative works must be made available to the world under the same rules used by Bioinformatics Journal. If copyright rules do not apply to articles published in Bioinformatics Journal, what rules do apply? Bioinformatics Journal uses a form of copyleft.
There are many different approaches to copyleft. The form of copyleft used by Bioinformatics Journal is the GNU Free Documentation License (GFDL). Before you submit your work to Bioinformatics Journal or publish your article in Bioinformatics Journal you should read the GFDL license.
How does wiki publishing under the GFDL protect your right to get credit and recognition for your intellectual work? Notice that every wiki page for articles at academia.wikicities.com has an associated "history". The history for an article documents the authors who contributed to the article and every edit to the article. The "history" is part of your article. The GFDL specifies that it "preserves for the author and publisher a way to get credit for their work." The "History" section of your wiki format article includes the "history page(s)" associated with your article. The GFDL requires that all copies of your article or derivative works containing part of your article include the "History" section of your wiki format article. If an article has a title page that lists the authors and if the "history page(s)" associated with the article do not indicate that there have been additional authors, then copies of the article can simply give credit and acknowledgement to the authors listed on the title page. For online copies of GFDL licensed wiki format material (text and images), it has become common practice to satisfy the requirement for crediting authors by providing a hypertext link back to the original wiki source(s) where the author history is stored electronically.
Multiple page articles. If it is convenient to place parts of your article on multiple wiki pages, use the following naming convention. If the first wiki page of your article has the name "This is my title", then give additional wiki pages for your article names like this: "This is my title: supporting data". Alternatively, you can specify on the first page of your article a short title. For example, if the full title is "This is my title", short titles could be "My title" or "TIMT". If you designate a short title, then give additional wiki pages for your article names like this: "Short title: supporting data". If your article has multiple wiki pages, list all of them on the first page of the article. You might want to make the first page of your article a title page and make use of the Bioinformatics Journal Title Page Outline. There is also an outline for the content part of your article: Bioinformatics Journal:Article Content Outline. Note: use of these outlines assumes you will be submitting you article to Bioinformatics Journal, as described in the next section, below.
Submit your article to Bioinformatics Journal[]
- If you want to submit an article to Bioinformatics Journal, you must register a user name' with Wikia. Help:Why Register
- You must associate your real (legal) name with your article. This is academic publishing and authors are expected to want proper recognition and attribution.
- You must provide a functioning email address in the Wikia registration system. #If you fail to respond to members of the Bioinformatics Journal community who are involved with publishing your article, Bioinformatics Journal might refuse to publish your article.
Note that Bioinformatics Journal distinguishes between submission of articles and formal publication of articles. Submission is not the same as formal publication. You have full control over the submission process. The Bioinformatics Journal community has its say in the decision to formally publish your article. The decision about formal publishing of your article is a statement by your peers about the quality and importance of your article.
The Bioinformatics Journal is an "open" journal. If you wish to bring an article you have written to the attention of the Bioinformatics Journal community, create a new page for your article at academia.wikicities.com and place the {{Bioinformatics Journal}} template at the start of your article. Help for using templates If you do not know how to work with the Wikia user interface, use the help feature. See the discussion of Multiple page articles at the end of the previous section (above) for another submission method.
You can draft and author your article in the wiki environment of this website. See preliminary drafts. Alternatively, you can construct your article in another format and then import it to wiki format.
You do not have full control over your article after you submit it. By placing your work on a page at academia.wikicities.com you agree that it is licensed under the GFDL. If you are at all uncertain what that means, go back to the top of this page and read about copyleft and the GFDL license.
You do not have full control over your article after you submit it because a copy of your article will always exist here and other people will be able distribute and make derivative works using the contents of your article. You do have control over the next step in the wiki publishing process. You decide when your article is ready for peer review.
The first author of a submitted article can designate co-authors who have the right to edit your article. The first author can also allow other members of the Bioinformatics Journal community to make minor corrections to your article (spelling, grammar, etc). To do so, mark your article with the {{Minor Edits Allowed}} template.
Multiple submissions. As the author of an article submitted to Bioinformatics Journal, you retain copyright to your materials (text you wrote, images you made). You can republish and reticence them in any way you like (with no effect on the GFDL version retained here). For example, you can submit a version of your article to a conventional print journal. However, most journals have a policy against publishing previously published articles and such policies might prevent them from publishing an article that you have previously published in wiki format under the GFDL. What about multiple submissions to wiki journals? Bioinformatics Journal has the policy that it will only accept articles that are submitted to one journal at a time. Bioinformatics Journal has a Bioinformatics Journal:Submitted elsewhere system for drawing the attention of the Bioinformatics Journal community to articles that have been submitted to other wiki journals. This allows authors who have submitted articles to other wiki journals to post a link to their article from Bioinformatics Journal:Submitted elsewhere. This will allow members of the Bioinformatics Journal community to learn of the existence of your article. Depending on the policies of other wiki journals, members of the Bioinformatics Journal community may be able to review your article as a submission to the other journal.
Peer Review[]
Bioinformatics Journal is a peer-reviewed journal. When your article is ready for peer review, use the Peer Review template.
Please note that there are special rules for articles that are peer reviews of other articles. If you wish to write a formal peer review article in which you critically evaluate an article marked by the {{Bioinformatics Journal}} template, you must mark your formal peer review article with the {{Bioinformatics Journal}} template. Formal peer review articles that review an article of the Bioinformatics Journal are themselves subject to peer review. See Bioinformatics Journal:Instructions for reviewers.
After you mark your article as an available target for peer review, you can respond to any peer review articles that are submitted as critiques of your article. You must do so by submitting a peer review article that critically evaluates the peer review article that is submitted as a critique of your original article.
You can also make modifications to your original article while it is under peer review. For example, if a reviewer makes a good suggestion about how to improve your article, you are free to modify your article in an attempt to improve your article and satisfy the reviewer. You are also free to either ignore the reviewer's suggestions or submit a rebuttal of the review. As mentioned above, if you think a reviewer is wrong, you give your rebuttal in the form of a new peer review article that is submitted as a critique of the peer review article that was targeted at your original article. Note: there are only two steps in the peer review process.
- The reviews of your original articles
- Your responses to those reviews (optional)
If a reviewer of your article wishes to discuss your rebuttal, the reviewer will do so in an appendix to their original review of your article.
Under the best of conditions, your article will be promptly reviewed by two reviewers and both will suggest that your article be published. If this happens, your article will qualify for "formal publishing" (see the next section, below).
Reviewers are expected to give detailed accounts of what they like and don't like about your article. Reviewers are also required to describe the scope of their review and give your article a ranking.
Scope of Reviews. The decision by Bioinformatics Journal about formally publishing your article requires at least two complete peer reviews of your article. Not all peer reviews are complete reviews. Some reviewers do not have competence or time to completely review your article, but they may be able to provide expert evaluation of parts of your article. Such partial reviews can be useful to the complete reviewers who will decide if your article should be formally published in Bioinformatics Journal.
Article rankings by peer reviewers. Peer review articles are expected to include a ranking of the reviewed article. Bioinformatics Journal uses a three value ranking system.
- Positive. If a reviewer gives a rank of "positive" this means that the reviewer wants your article to be formally published by Bioinformatics Journal. However, the reviewer can give your article a positive ranking while still requiring certain changes to your article. Generally such requirements must involve only minor alterations to your article.
- Neutral. A ranking of "neutral" means that the reviewer sees value in your article, but the reviewer is unable to recommend formal publication until you address concerns listed by the reviewer. Reviewer concerns might include questions that you must answer in a rebuttal or changes that you are asked to make in your article.
- Negative. A ranking of "negative" means that the reviewer does not want to see your article formally published in Bioinformatics Journal. A reviewer who gives your article a negative ranking must explain what is wrong with your article. In the worst case, the reviewer may feel that your article is a complete disaster and may resent the fact that they wasted time reading it. Such a reviewer response can have serious implications if it is backed up by similar responses from other reviewers.
If two reviewers agree that your article is a waste of time, the Bioinformatics Journal community may decide that any future article submissions from you require prescreening. In the worst case, the reviewers might both judge that you are spamming the journal and you might be told that future submissions are not welcome.
If only one of the first two complete reviewers of your article decides that your article should be published, then at least one more complete review might be required as a tie breaker. If neither of the first two reviewers gives your article a negative ranking, then you have the option of withdrawing your submission, trying to rebut the reviewers, or modifying your article in an attempt to satisfy the reviewers.
If one reviewer is positive or neutral but a second reviewer is negative, then you can try to rebut the negative reviewer. If a negative reviewer does not change their ranking of your article after reading your rebuttal, you can wait for a third tie-breaking reviewer to critique your article or you can withdraw the submission and try to publish in a different journal.
If there are more than two complete reviewers of an article and some reviewers rank the article as positive and others rank it as negative, then a cancellation rule goes into effect. One positive ranking cancels one negative ranking. A net ranking of two or more positives (after all negatives have been cancelled by additional positives) is required for formal publication.
A net ranking of two or more negatives (after all positives have been canceled by additional negatives) is a rejection of the article. There is a chance that you can successfully rebut the negative reviewers, or you might decide to withdraw the submission and take your article to another journal.
Negative rankings of submitted articles are always a serious matter. This is true of articles that are themselves peer reviews. As mentioned above, authors who submit an article for peer review can in turn review the peer review articles that critique the originally submitted article. The same three-valued (positive, neutral, negative) ranking system is applied to peer review articles. However, these rankings are used in different way than are the ranking of regular articles. Any member of the Bioinformatics Journal community can perform peer reviews. Peer review of peer review articles is important to the Bioinformatics Journal community. Peer review of peer review articles is a form of quality control for the peer reviewers themselves.
- Two negative rankings of a peer review article can cancel that peer review article's utility as part of a decision for formal publication of an article. For example, if two members of the Bioinformatics Journal community submit peer review articles that give negative rankings of an earlier peer review article, this can cancel the effect of that earlier peer review article. A negative ranking of another peer review article is a warning sign to the Bioinformatics Journal community that there may be a problem with a reviewer. A negative ranking of a peer review article must be accompanied by explicit description of error, bias, misconduct or poor judgment on the part of the original reviewer.
- Neutral rankings of a peer review article must be accompanied by specific suggestions for reconsideration on the part of the original reviewer. This is a form of questioning the judgment of another reviewer or bringing a new perspective to the attention of another reviewer.
- Positive rankings of a peer review article are a vote of confidence in favor of the original reviewer. One positive ranking of a peer review article can cancel the effect of one negative ranking. This can be important if the Bioinformatics Journal community is contemplating restrictions on a reviewer who has received negative rankings for past peer review articles.
Formal publishing[]
As described above, if the peer review process determines that there is a consensus in favor of publication of an article, then formal publication becomes possible. In general, this means that there are two more positive reviewers of the article than negative reviewers. When the reviewers of an article agree that the author of the article has made adequate modifications in response to the requests of the reviewers, then a reviewer can mark the article with the Bioinformatics Journal Published Article template.
What happens after formal publishing?
Other authors can begin to make citations to your article after it is formally published. As discussed below, sometimes formally published wiki articles can change after publication, so citations to wiki journal articles should always explicitly cite the date of a specific version of the article.
After formal publishing, the first author of an article still has some control over the article. Some authors may decide to never allow future editing of a formally published article. Other authors may leave an article marked as open for Minor edits in order to allow the Bioinformatics Journal community to continue to correct minor errors in the article. For some articles, particularly literature review articles, authors may decide to periodically update the content of the article. In some cases, the first author may be open to adding new co-authors after formal publication who would assist in keeping the article updated and up to date as a review of the literature.
The Bioinformatics Journal also allows peer review to continue after formal publication of an article. This can be important for several reasons. Errors might be found in an article only after it has been formally published. Also, for articles that are updated by their author(s) after formal publication, new errors or problems might arise that warrant critical evaluation by the Bioinformatics Journal community.