Open Development Model Research Articles

XCP-D: A Robust Pipeline for the Post-Processing of fMRI data

Abstract Functional neuroimaging is an essential tool for neuroscience research. Pre-processing pipelines produce standardized, minimally pre-processed data to support a range of potential analyses. However, post-processing is not similarly standardized. While several options for post-processing exist, they may not support output from different pre-processing pipelines, may have limited documentation, and may not follow generally accepted data organization standards (e.g. BIDS). In response, we present XCP-D: a collaborative effort between PennLINC at the University of Pennsylvania and the DCAN lab at the University of Minnesota. XCP-D uses an open development model on GitHub and incorporates continuous integration testing; it is distributed as a Docker container or Apptainer image. XCP-D generates denoised BOLD images and functional derivatives from resting-state data in either NIfTI or CIFTI files following pre-processing with fMRIPrep, HCP, or ABCD-BIDS pipelines. Even prior to its official release, XCP-D has been downloaded >5,000 times from DockerHub. Together, XCP-D facilitates robust, scalable, and reproducible post-processing of fMRI data.

FESetup: Automating Setup for Alchemical Free Energy Simulations.

FESetup is a new pipeline tool which can be used flexibly within larger workflows. The tool aims to support fast and easy setup of alchemical free energy simulations for molecular simulation packages such as AMBER, GROMACS, Sire, or NAMD. Post-processing methods like MM-PBSA and LIE can be set up as well. Ligands are automatically parametrized with AM1-BCC, and atom mappings for a single topology description are computed with a maximum common substructure search (MCSS) algorithm. An abstract molecular dynamics (MD) engine can be used for equilibration prior to free energy setup or standalone. Currently, all modern AMBER force fields are supported. Ease of use, robustness of the code, and automation where it is feasible are the main development goals. The project follows an open development model, and we welcome contributions.

Geocomputation and Open Source Software: Components and Software Stacks

Geocomputation, with its necessary focus on software development and methods innovation, has enjoyed a close relationship with free and open source software communities. These extend from communities providing the numerical infrastructure for computation, such as BLAS (Basic Linear Algebra Subprograms), through language communities around Python, Java and others, to communities supporting spatial data handling, especially the projects of the Open Source Geospatial Foundation. This chapter surveys the stack of software components available for geocomputation from these sources, looking in most detail at the R language and environment, and how OSGeo projects have been interfaced with it. In addition, attention will be paid to open development models and community participation in software development. Since free and open source geospatial software has also achieved a successively greater presence in proprietary software as computational platforms evolve, the chapter will close with some indications of future trends in software component stacks, using Terralib as an example.

A "bottom up" governance framework for developing Australia's marine Spatial Data Infrastructure (SDI)

Spatial Data Infrastructures (SDIs) have been developing in some countries for over 10 years but still suffer from having a relatively small installed base. Most SDIs will soon converge around a service-oriented-architecture (SOA) using IT standards promulgated primarily by the Open Geospatial Consortium (OGC) and ISO Technical Committee 211. There are very few examples of these types of architected SDIs in action, and as a result little detailed information exists on suitable governance models. This paper discusses the governance issues that are posed by SOA-based SDIs, particularly those issues surrounding standards and services management, with reference to an Australian marine case study and the general literature. A generalised governance framework is then postulated using an idealised use case model which is applicable for bottom-up, community-based initiatives. This model incorporates guiding principles and motivational and self-regulation instruments that are characteristically found in successful open source development activities. It is argued that harnessing an open development model, using a voluntary workforce, could rapidly increase the size of the SDI installed base and importantly defray infrastructure build costs.

Open Science: Open Source Licences in Scientific Research

The use of non-proprietary software licenses - such as the Free Software (FS) and Open Source Software (OSS) license models - is definitely on the increase, showing that the open development models are viable and sometime even commercially successful systems. Amongst these models, one of the most interesting licenses is that offered by so-called copyleft licenses, which are licenses that allow software to be transferred with the insurance that the source code will remain open, with the caveat that anyone who redistributes the software, with or without changes, must pass along the freedom to further copy and change it. However, software development is not the only area in which this licensing model could apply. The viral nature of copyleft licenses has generated a considerable amount of interest in circles that transcend software development. The idea of sharing materials is not new, and has been made more evident by the chaotic and sometimes anarchic nature of the internet. However, shared materials tend to suffer from the possibility of third parties that use the freely acquired information to turn them into proprietary works. That is why many different organisations are turning to the copyleft model to protect works that are being freely shared online. One such project is the OpenContent License (OPL), a collaborative effort that sets a similar license to the GPL, ensuring that shared works will continue to remain free to subsequent users. A more ambitious project is the Creative Commons, which offers a wide range of licenses applicable to all sorts of creative material. In the area of biotechnology, there have been some suggestions that the copyleft model could be used to protect the public results of the human genome race being placed in the public domain by several researchers, something that has been suggested by a leading member of the Human Genome Consortium, although the idea has never been implemented. This paper will explore the application of copyleft licenses to other areas of research and development, and will try to explore if these can be successfully adapted to various different areas where creators want to share their works to the public but want to make sure that there will not be any further commercialisation of their creations.

Towards microbial data integration

There are currently 100–200 microbiology-related databases in existence, although it is impossible to find answers to queries that span even a few of these. The Center for Microbial Ecology (CME) at Michigan State University seeks to change this situation by coordinating the creation of an Integrated Microbial Database (IMD), accessible through the World Wide Web (WWW). Such a system will contain up-to-date phylogeny and taxonomy, gene sequences (including genomes), biochemical data, metabolic models, ecological and phenotypic data. Current main obstacles to creation of an IMD are the lack of a single freely available organismal nomenclature with synonyms and the availability of much critical data. An IMD will have major impacts on microbial biology: currently intractable fundamental questions might be answered, experiments could be refocused, and new commercial possibilities created. An IMD should remain freely available and be created under an open development model.