The Future of Scientific Publishing : Is Here, Now

March 13, 2011

Enough of criticizing the decadent Conferences and Journals that insist on using obsolete practices unfit for the Digital Age.

Instead of ranting about them, this time, let’s take a look at the progressive Journals that are the Future of Scientific Publishing.

As Clay Shirky said:

               “Free Cultures get what they Celebrate !”

So, let’s then celebrate the Journals that are doing the right thing

                                   PLoS ONE

Top Features

  • Open Access
  • Peer-Review by readership
  • Community structure
  • Fully On-Line publication
  • Guidelines for verifying REPRODUCIBILITY
  • Requirements for Data Sharing
  • Requirements for Software Sharing
    • Under Open Source software licenses
      • PLoS ONE supports the development of Open Source software and believes that for submissions in which software is the central part of the paper, then adherence to appropriate Open Source standards will ensure that the submission will conform to our requirements which state that “methods must be described in sufficient detail so that another researcher is able to reproduce the experiments described” as well as our “aim to promote openness in research and intention that all work published in PLoS ONE can be built on by future researchers.” Therefore, if new software or a new algorithm is central to a paper, authors must confirm that the software conforms to the definition of Open Source as defined by the ten rules of the Open Source initiative and have deposited the following in an open software archive as well as included as supplemental information with the article:
        1. The associated source code of the software described by the paper: This should, as far as possible, follow accepted community standards and be licensed under a suitable license such as BSD, LGPL or MIT (see for a full list). Dependency on commercial software such as Mathmatica and Matlab does not preclude a paper from consideration, although complete Open Source solutions are preferred.
        2. Documentation for running and installing the software: For end user applications instructions for installation and using the software are prerequisite; for software libraries instructions for using the API are prerequisite.
        3. A test dataset with associated control parameter settings: Where feasible, results from standard test sets should be included. Where possible test data should not have any dependencies; for example, a database dump.

      A condition of acceptance is that the software can be run by reviewers accessing the public software and that results presented in the paper are reproducible. The software only need run on one hardware/software platform in common use by the readership (including Matlab), although it must run without dependencies on proprietary or otherwise unobtainable ancillary software. Articles describing software that requires access to databases and other resources whose persistence is not guaranteed (e.g., individual laboratory databases without funding support) will not be considered.

      In addition, the results described in the paper must be reproducible when peer reviewers, editors, or readers run the software on the deposited dataset and with the provided control parameters.



Main Features

                                      Open Research Computation
                                           (from BiomedCentral)

Main Features

  • Open Access (as all BiomedCentral Journals)
    • Authors retain the  copyright of their papers
    • Papers are freely available under the BioMedCentral license
  • Reproducibility Verification
    • Software: “Open Research Computation differs from other journals with a software focus in its requirement for the software source code to be made available under an Open Source Initiative compliant license, and in its assessment of the quality of documentation and testing of the software.”
    • Data: Open Research Computation has very high standards for data availability and reproducibility. It is expected that all the data, code, and software required to reproduce any examples in the paper will be made freely available for download from an appropriate recognized repository or the journal website.
  • Review criteria for Source Code
    • Code and License
      • Is the source code as well as executables and/or an instance of the service (of a clearly defined version) available on appropriate public repository?
      • Is the source code made available under an Open Source Initiative ( compliant license? Specifically users must have the right to examine, compile, run and modify the code for any purpose.
      • Are project authors and contributors clearly defined, ideally through a Description of a Project [,] document? We recommend the use of the automatic DOAP generator such as those linked here:


      • Is the source code thoroughly documented both externally (Readme, external documentation) and internally (within the code)?
      • Are all public methods/functions/classes in the submitted code documented?
      • Is documentation consistent with best practice guidelines for the language and/or research domain?
      • Are all dependencies on external libraries, frameworks (proprietary or otherwise) clearly documented?
      • Are detailed instructions for compiling, deploying, and testing the software provided?


      • Does the source code/package contain a full test set, ideally automated using a standard unit test framework for the language?
      • Does the test set have 100% coverage of public functions and classes?
      • Is the test methodology and implementation consistent with best practice guidelines for the language and/or research domain?


      • Are example input data, output data, and detailed instructions on use provided?
      • Are test input and output data provided for all use case examples given in the paper?
      • Are all datasets required for testing or validation provided or available along with the expected output?


Main Features

  • Mission
    We believe that biomedical publishing has not been able to keep pace with advancing technology. Biomedical publishing needs radical changes to empower authors, reviewers and readers. We therefore would like to introduce a novel method of post publication peer review, which is author driven and facilitates rapid publication at no cost to the readers and authors.
  • Author Driven
    Authors are in charge of the entire publication and review process. Traditionally biomedical journals have published articles from authors at no cost and then delivered them to readers at a price.
  • Post-publication peer-review
    • Conventional peer review system hinders transparent scientific communication, delays the publication process and adds to the cost of publishing.
  • Aware of the Internet

                            This is the Future.

These are the traits of a REAL Scientific Publishing system.

                       They are Here, Now.

If the Journals and Conferences where you

  • Publish
  • Review
  • Cite
  • Subscribe

Do not look like this,
then you are living in a world doomed to extinction.

You are keeping an obsolete system alive…
and delaying the most significant scientific revolution of this century.

Just know,
that you indeed have a choice,
and it is Here and Now. 

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