Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Preprint servers and open journals

    28th February 2016

    Let’s start with some definitions.

    With Open Journals I’m referring to open/public peer-review journals.
    With preprint servers, I’m referring to services which allow you to publish your manuscript with a DOI, for pre-submission interest and feedback collection.

    I am aware of the following public peer-review journals:

    • F1000 Research: your submission is made public without any editorial pre-screening within an average of 7 days, but only gets indexed in PubMed/Scopus/Scholar after a successful public peer review. Public means that a reviewer-signed evaluation appears together with the submitted manuscript. Authors may respond to criticism, and upload revisions of their submission. I believe a submission passes peer review after two positive reviews. Note that even your initial submission receives a DOI, and is thus citable (as well as all subsequent revisions). Brief examination of articles in some of the topics tells me that F1000 Research is a good place to publish, esp. because it is a kind of pre-print + journal in one package. You pay per-submission, there are 3 tiers by word count.
    • The Winnower: submit-review-revise, but here you pay for the DOI after your submission is reviewed. Before review your submission is thus not citable (except for by URL, which isn’t tracked as easily as DOI references). I haven’t formed an opinion on how attractive the winnower is for submitting, but I did find this quite interesting story for you to enjoy :)
    • Science Open: this project encompasses 5 mostly medical journals. It lists over 11 million articles on the front page, but those are sourced from other publications; Science Open itself seems to have several hundred publications across all 5 journals. Submissions get a DOI, then can undergo public review. It is not clear to me in which direction Science Open will be moving – towards becoming an excellent research papers aggregator, or towards becoming a publishing platform, or – like now – towards both.

    I’m also aware of the following preprint servers:

    • arXiv: probably the oldest one, suitable for quantitative research. Submissions are pre-screened to meet certain minimal requirements.
    • bioRxiv (CSHL): preprint server for biology. Submissions are pre-screened to meet certain minimal requirements.
    • figShare: online repository for digital artifacts, including figures, datasets, tables, PDF files et cetera. Uploaded items get a DOI. I used to think that you have to pay for a DOI, but right now this feature is listed under free account features.
    • PeerJ preprints (and PeerJ journal): preprints are free, and you can submit a PeerJ preprint to PeerJ with a single button click. PeerJ has two journals, PeerJ itself (Life, Bio, Health) and PeerJ Computer Science. As is common, manuscript submitter pays for open access article. PeerJ has several different schemes of payment, including per-article, author membership, and institutional subscription. PeerJ has approximately 1800 articles published.
    • Zenodo is a DOI-providing repository similar to FigShare, powered by Horizon-2020 EU program funding and CERN’s Data Centre.

    So far I only had experience with BioRxiv, and it was great. I’ll consider F1000 Research or PeerJ for some of my next manuscripts – both models are quite attractive, especially F1000′s open review.

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