Here is an excerpt from the announcement:

With support from the NIH National Library of Medicine, ISP allows authors to publish large 2D and 3D datasets with original source data that can be viewed and analyzed interactively by readers. ISP provides the software for authors to organize and publish source data while offering readers the viewing and analysis tools.

• MIDAS, the repository: here are the terms of use:

… You may use the datasets for research purposes, provided that Author(s) are given proper credit as the source of the data, in a manner consistent with generally accepted scientific principles. …

• OSA-ISP, the software: only available for Windows and Mac OS, and doesn’t seem to be open source. Moreover, access to full OSA ISP authoring functionality is freely available, following activation, only for 30 days. After 30 days, the software reverts to reader mode. Here is the ISP- FAQs.

You can give them your feedback by taking their survey.

Post from: Reproducible Research Planet Blog

Post Link: %%OSA Interactive Science Publishing (ISP) and MIDAS%%

Here is an excerpt from the announcement:

The Office of Science and Technology Policy in the Executive Office of the President and the White House Open Government Initiative is launching a “Public Access Policy Forum” to invite public participation in thinking through what the Federal government’s policy should be with regard to public access to published federally-funded research results. To that end, OSTP will conduct an interactive, online discussion beginning Thursday, December 10. We will focus on three major areas of interest: Implementation, Features, and Management.

In the implementation section we read:

One of our nation’s most important assets is the trove of data produced by federally funded scientists and published in scholarly journals. The question that this Forum will address is: To what extent and under what circumstances should such research articles—funded by taxpayers but with value added by scholarly publishers—be made freely available on the Internet?

Many interesting comments have been made on this subject encouraging open access to the published papers as well as any supporting data and code.

Here are some short excerpts from the numerous comments:

[…] It is imperative to provide public access to tax-payer funded scientific output, not only the final published paper but also the supporting data and code necessary for the reproducibility and skepticism fundamental to scientific communication and progress.

[…] It is most feasible to open access to the data after the data-taking has completed, the data are understood, and a simple format can be provided to the public.

[…] Any embargo should be as short as possible (preferably none!), but all articles must be deposited in an institutional repository right away, upon date of acceptance, not just after the embargo elapses: there will be 2 kinds of OA documents in the archive: immediate OA (at least 63% of journals endorse immediate OA) and delayed OA (embargoed ).

[…] What version of the paper should be made public under a public access policy (e.g., the author’s peer-reviewed manuscript or the final published version)?
Both— the author’s peer-reviewed manuscript prior to publication and the final published version after publication. The heart of science is the testability of hypothesis. To this end all raw data should be included with the manuscript. The goals of open government should support the objective of keeping the science honest and testable.

[…] Some suggest that every portion of a research effort should be made public— all collected or raw data, notebooks, calculations, etc. There is a case to be made for publishing data sets. However, requiring everything recorded during a research effort be prepared for public access may have the perverse effect of slowing the publication process, or discouraging publication of some research all together. Making the published article accessible is a more reasonable and achievable first goal, followed by publishing pertinent datasets when it is decided how best to do so.

Many other interesting suggestions can be found on the OSTP blog.

Post from: Reproducible Research Planet Blog

Post Link: %%Thoughtful Comments on Public Access to Research Publications%%

Here is an excerpt from the announcement:

The Journal of Experimental Linguistics is part of the Linguistic Society of America’s eLanguage initiative. Like the rest of eLanguage, JEL is an Open Access online journal.

JEL is a linguistic “journal of reproducible research”, that is, a journal of reproducible computational experiments on topics related to speech and language. These experiments may involve the analysis of previously­ published corpus data, or of experiment­-specific data that is published for the occasion. Other relevant categories include computational simulations, implementations of diagnostic techniques or task scoring methods, methodological tutorials, and reviews of relevant new publications (including new data and software).

Mark Liberman is the editor in chief.

Post from: Reproducible Research Planet Blog

Post Link: %%JEL— a linguistic journal of reproducible research%%

Here is an excerpt from the announcement:

The Open Database License (ODbL) is an open license for data and databases which includes explicit attribution and share-alike requirements.

This license, the first of its kind, is a major step forward for open data. There are currently very few licenses available suited to data and databases and none which provide for share-alike (existing share-alike licenses such as the GPL, GFDL and CC By-SA are all unsuitable for data).

The development of the ODbL, has been a major effort extending over more than one and half years with an intensive consultation and review period for the last 6 months.

Post from: Reproducible Research Planet Blog

Post Link: %%Open Database License is Released%%

In such a distributed system, good visibility and retrieval of information are essential for the successful delivery of services. Fortunately, many different systems have been established to improve the information retrieval, notably search engines.

While search engines are vital for the retrieval of information on the Web, they do not index websites equally and may not index new pages for months. This usually leads to a delay in the information retrieval whereas delayed indexing of scientific research is not desirable …

|Read The Full Article|

Post from: Reproducible Research Planet Blog

Post Link: %%Enhance the Visibility of Your Reproducible Research Compendia%%

Here is an excerpt:

What is Open Data?

Open data is data that anyone is free to use, reuse and redistribute without restriction (except, perhaps the requirements to attribute and sharealike). For precise details see http://opendefinition.org/.

Why Does Openness and Licensing Matter?

[…] open data is  crucial because open data is so much easier to break-up and recombine, to use and reuse. Licensing is important because it removes uncertainty. […]

• So How Can I Make My Data Open?
• How Do I License My Data?

Post from: Reproducible Research Planet Blog

Post Link: %%A Guide to Making Your Data Open%%

• Sweave -Create dynamic reports (based on LaTeX and R)
• SCons- A part of the Madagascar software package, based on SCons, for managing data processing flows and reproducible computational experiments
• StatDocs-Create interactive statistical documents
• DynDoc-A set of functions to create and interact with dynamic documents and vignettes in R
• MATLAB Report Generator- Automatically generate reports from MATLAB in a wide variety of formats
• Cacher and CacheSweave-R packages for caching statistical analyses and Sweave computations
• Python Tools for RR-Python tools for reproducible research on hyperbolic problems
• Emacs Speaks Statistics-Supports editing of scripts and interaction with various statistical analysis programs such S-Plus, R, SAS and Stata

If you are aware of other tools with a focus on reproducibility, simply write a comment on this post to share it with everyone.

[Updates]

• AMRITA-A system for communicating software-based ideas and information. It operates as a cross between a document preparation system, a computational engine, and a programming language (does not run under Windows)

Post from: Reproducible Research Planet Blog

Post Link: %%Reproducible Research Tools%%

Here is an excerpt from the introduction:

The Policy-making for Research Data in Repositories: A Guide is intended to be used as a decision-making and planning tool for institutions with digital repositories in existence or in development that are considering
adding research data to their digital collections.

The guide is a public deliverable of the JISC-funded DISC-UK DataShare project (2007-2009), http://www.disc-uk.org/datashare.html, which established institutional data repositories and related services at the partner institutions: the Universities of Edinburgh, Oxford and Southampton. It is a distilled result of the experience of the partners, together with Digital Life Cycle Research & Consulting. The guide is one way of sharing our experience with the wider community, as more institutions expand their digital repository services into the realm of research data to meet the demands of researchers who are themselves facing increasing requirements of funders to make their data available for continuing access.

Post from: Reproducible Research Planet Blog

Post Link: %%A Guide to Including Research Data in Repositories%%

Reproducible Research Librum is an in-depth approach to provide a comprehensive list of reproducible research websites and compendia.

In brief, Librum aims to increase the visibility of reproducible research compendia over Internet and to facilitate the search and find process for end-users.

|Go to Librum| |Learn more about Librum|

Post from: Reproducible Research Planet Blog

Post Link: %%Reproducible Research Librum_beta is going live!%%

How to Best Share?

• Self-Archiving— Providing Open Access to the Research Paper
• Open Licensing— Providing Open Access to the Code and Data

[…]

|Read The Full Article|

Post from: Reproducible Research Planet Blog

Post Link: %%How to Best Share Your Reproducible Research Compendium%%