Clinicalcodes.org Exchange

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The clinicalcodes.org repository holds code lists for published electronic medical record studies (i.e. the coded descriptions of study cohorts). The goal of clinicalcodes.org is support replication of previously published studies. Using the Research Object model, an export of a study packages codes, study, and metadata together to support exchange. An Example RO exported in this manner… Read more »

RO Bundle (Zip)

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The RO Bundle specification defines a file format for storage and distribution of Research Objects as a ZIP archive; called a Research Object Bundle (RO Bundle). RO Bundles allow capturing a Research Object to a single file or byte-stream by including its manifest, annotations and some or all of its aggregated resources for the purposes of exporting, archiving, publishing and… Read more »

iPython Notebooks

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  The IPython Notebook is a web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document: These notebooks are normal files that can be shared with colleagues, converted to other formats such as HTML or PDF, etc. You can share any publicly available notebook by… Read more »

Nanopublications

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Nano publications provides a model and vocabulary for describing a scientific statement – along with the context for that statement – in a machine readable manner.   From nanopub.org: A publication is the smallest unit of publishable information: an assertion about anything that can be uniquely identified and attributed to its author. Individual nanopublications can… Read more »

Research Object (RO) Model

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RO Model Core The core concepts of research objects, identity, aggregation, and annotation, are captured in the specification of the ro model. The specification of this core research object model is described in the ro ontology under the namespace http://purl.org/wf4ever/ro#. Extensions There are also the following ontology implementations of extensions to the core research object model: The roevo model… Read more »

ReproZip

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Reprozip is a project led by Prof. Juliana Freire at NYU, to develop a tool that makes it easier for authors to publish reproducible results and for reviewers to validate these results. By tracking operating system calls, ReproZip systematically captures detailed provenance of existing experiments, including data dependencies, libraries used, and configuration parameters. This information is combined… Read more »

Combine Archive

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“A COMBINE archive is a single file containing the various documents (and in the future, references to documents), necessary for the description of a model and all associated data and procedures. This includes for instance, but not limited to, simulation experiment descriptions, all models needed to run the simulations and associated data files. The archive is encoded… Read more »

Code as a Research Object

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Code as a Research Object is a joint initiative between the Mozilla Science Lab, figshare and GitHub. figshare and GitHub two leading repositories for data and code. The project has built a bridge to allow users to push code from their GitHub repository to figshare, providing a Digital Object Identifier for the code.