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BOSC 2019, the 20th annual Bioinformatics Open Source Conference

The Bioinformatics Open Source Conference is a volunteer-organized meeting that covers open source software development and open science in bioinformatics. Launched in 2000, BOSC has been held every year since. BOSC 2019, the 20th annual BOSC, took place as one of the Communities of Special Interest (COSIs) at the Intelligent Systems for Molecular Biology meeting (ISMB/ECCB 2019). The two-day meeting included a total of 46 talks and 55 posters, as well as eight Birds of a Feather interest groups. The keynote speaker was University of Cape Town professor Dr. Nicola Mulder, who spoke on “Building infrastructure for responsible open science in Africa”. Immediately after BOSC 2019, about 50 people participated in the two-day CollaborationFest (CoFest for short), an open and free community-driven event at which participants work together to contribute to bioinformatics software, documentation, training materials, and use cases.

97 MATHEMATICS AND COMPUTING↗

Development of a Distribution Optimal Power Flow Federate for Open-Source OEDI-SI Platform

Increasing numbers of distributed generators in the electric power distribution networks require developing a control strategy to optimize solutions in real time. Linearized optimal distribution flow development has seen growth and acceptance in the distribution systems literature for efficiently modeling the \glspl{opf} for distribution systems. This paper examines the implementation and integration procedure for linearized optimal distribution flow federate to \gls{oedisi} platform. Specifically, we discuss i) the usage of the \gls{oedisi} platform, ii) obtaining a tractable solution using developed \gls{opf} federate, and iii) validation of solutions and bench-marking the \gls{oedisi} platform with developed \gls{opf} federate using OpenDSS. In brief, we demonstrate how a general linearized optimal distribution flow federate can be developed and integrated with a co-simulation environment to mimic real-world examples. The efficacy of the proposed method is demonstrated using the IEEE 123-bus test system under different scenarios to obtain a tractable solution and compare its results.

Sadnan, Rabayet↗

A Platform for Innovation and Standards Evaluation: a Case Study from the OpenMRS Open-Source Radiology Information System

Open-source development can provide a platform for innovation by seeking feedback from community members as well as providing tools and infrastructure to test new standards. Vendors of proprietary systems may delay adoption of new standards until there are sufficient incentives such as legal mandates or financial incentives to encourage/mandate adoption. Moreover, open-source systems in healthcare have been widely adopted in low- and middle-income countries and can be used to bridge gaps that exist in global health radiology. Since 2011, the authors, along with a community of open-source contributors, have worked on developing an open-source radiology information system (RIS) across two communities—OpenMRS and LibreHealth. The main purpose of the RIS is to implement core radiology workflows, on which others can build and test new radiology standards. This work has resulted in three major releases of the system, with current architectural changes driven by changing technology, development of new standards in health and imaging informatics, and changing user needs. At their core, both these communities are focused on building general-purpose EHR systems, but based on user contributions from the fringes, we have been able to create an innovative system that has been used by hospitals and clinics in four different countries. We provide an overview of the history of the LibreHealth RIS, the architecture of the system, overview of standards integration, describe challenges of developing an open-source product, and future directions. Our goal is to attract more participation and involvement to further develop the LibreHealth RIS into an Enterprise Imaging System that can be used in other clinical imaging including pathology and dermatology.

61 RADIATION PROTECTION AND DOSIMETRY↗

The 2017 Bioinformatics Open Source Conference (BOSC)

The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017 ) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year’s theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.

59 BASIC BIOLOGICAL SCIENCES↗

BOSC 2025, the 26th Bioinformatics Open Source Conference

The 26th annual Bioinformatics Open Source Conference (BOSC 2025, open-bio.org/events/bosc-2025) brought its community-driven focus on open-source bioinformatics and open science to the 2025 conference on Intelligent Systems for Molecular Biology and the European Conference on Computational Biology (ISMB/ECCB 2025). Since its launch in 2000, BOSC has been the premier annual meeting covering open-source bioinformatics and open science. Framed by two keynote addresses and a thought-provoking panel discussion, the two-day conference included sessions dedicated to open data, analytic tools and pipelines, workflow platforms, knowledge representation, and the application of AI/ML. The first keynote talk was delivered by Christine Orengo: “Working together to develop, promote and protect our data resources: Lessons learnt developing CATH and TED.” A joint session with the Bio-Ontologies and Knowledge Representation (BOKR) track the second day of BOSC started with a keynote talk by Chris Mungall entitled “Open Knowledge Bases in the Age of Generative AI”. A closing panel on Data Sustainability, moderated by Mónica Muñoz Torres, featured panelists Scott Edmunds, Varsha Khodiyar, Tony Burdett, Nicky Mulder, and Chris Mungall. This year, the CollaborationFest collaborative work event that typically precedes or follows ISMB was incorporated as part of the main conference and organized by BOSC with help from the Function and 3D-SIG tracks.

bioinformatics↗

NASA WorldWind: Open Source Visualization Technology for Earth Observation

NASA WorldWind: Open Source Visualization Technology for Earth Observation WorldWind, open source virtual globe technology for Java, iOS, Android and Web, is provided by NASA and is architected as API-centric modular componentry. This enable it to be continually optimized and feature-enriched in ways that allow applications based on this SDK (Software Development Kit) to benefit Earth Observation, especially Open Science, with minimal or no adjustment for the decade ahead. The next-generation National Airspace System (NAS) aviation management system for the U.S. Federal Aviation Administration, FAA, uses WorldWind, as do applications currently being developed by the European Space Agency, along with several other US and European government agencies and industry partners. This presentation will demonstrate several NASA open source use cases for WorldWind technology that include advances being made to optimize access to NetCDF and HDF data via WebWorldWind.NASA WorldWind: Multidimensional Geospatial Web Platform The ability to see spatial data in its native context is essential for that data to be appreciated whether by the scientific community, policy and decision-makers or the general public. Recently, the accessibility of spatial data has dramatically improved. Without the need to install an application, spatial data can now be experienced via any web browser, mobile devices included. For developers, by simply updating the app on your server, the latest version of your application is now immediately available to your entire usercommunity. Unlike other virtual globes such as Google Earth, NASA World Wind offers something very special, full control to customize the interface with any features or functionalities you might need. You decide how the data is accessed and experienced. This allows you to provide maximum value of the information to your user community. The web version of NASA WorldWind (WebWorldWind) has made it possible for a whole new suite of applications for managing and sharing spatial data. Apps built with this web version are ideal for immediate social media type activity and also facilitate delivery of sophisticated data exchange scenarios such as weather and climate research, disaster response, personal navigation, and industrial-strength tracking for transportation, supply chain, aviation and satellites. WebWorldWind is an application component, not an app in itself. It is written in JavaScript and provides the real world geographic context for spatial data and information visualization, using a rich set of shapes and graphic primitives. WebWorldWind also provides platform independence, while accommodating any number of data types. Web WorldWind runs on any platform via a browser, i.e., Internet Explorer, Firefox, Chrome and Safari. Features include, 3D virtual globe, 2D map with multiple projection choices (Mercator, Polar, UPS, Equirectangular), imagery and elevation import, extensible, data retrieval (via REST, WMS, WCS, WFS, Bing, User-Defined), decluttering, measurement, accurate line-ofsight, subsurface visualization, and more.

Open Source Mapping↗

IM3 Open Source Data Center Atlas

IM3 Open Source Data Center Atlas Description This dataset contains locations of existing data center facilities in the United States. Data center locations were derived from OpenStreetMap (OSM), a crowd-sourced database. Data points from OSM are processed in various ways to determine additional variables provided in the data including: facility area (square feet), associated US county, and US state. This dataset can be used to identify areas of concentrated data center development and inform government and private sector planning strategies for future buildout of data centers and the infrastructure necessary to support it. Usage Notes Validation of OSM-derived data center locations is an ongoing development under the IM3 project, and the database will be updated as new information becomes available. In some instances, both the data center area (e.g., campus) and individual data center buildings are included as overlapping areas in the database. Both values are retained. Data center points, buildings, and campus areas are provided as separate layers in the downloadable data package. Note that data items are not necessarily complete across layers. That is, a specific data center may only be present as a single point geometry in the "point" layer while other data centers are represented in both the campus and building layers. In some cases, data center campuses and/or buildings straddle a county boundary line. Mappings to both counties are retained in the database as separate rows. These data rows will have the same data center id information, but each will have different county information. Crowd-sourced data, by nature, relies on individuals and communities to provide information. As a result, some data may be missing where it has not yet been reported. As we collect information on additional data center locations and as OSM receives additional contributions, the database will be updated to capture additional data points not yet shown. Technical Information Data is available for download under the following formats: GeoPackage (GPKG) CSV Geospatial data is provided in the WGS84 (EPSG:4326) coordinate reference system. The GeoPackage download contains the following layers. See usage notes for more information. "point" "building" "campus" The "point" layer includes all data from OSM that had POINT geometry type (i.e., individual coordinates). The "building" layer includes all OSM data that did not have POINT geometry and where the building tag in the OSM export was neither equal to "no" or null. Data that did not meet the "point" or "building" qualification was assumed to be a facility campus and included in the "campus" layer. The dataset contains the following parameters. Variables provided by OSM are labeled with (OSM-provided). id - unique identification number (OSM-provided with prefix of "node/", "relation/" and similar attributes removed) state - name of US state state_abb - two letter US state abbreviation state_id - state ID number county - name of US county county_id - county ID number ref - reference numbers or codes (OSM-provided) operator - the name of the company, corporation, or person in charge facility (OSM-provided) name - name of facility (OSM-provided) sqft - surface area of facility polygon, measured in square feet. Only available for "building" and "campus" layers lat - latitude of data centroid point lon - longitude of data centroid point type – represented spatial information. One of "point", "building", or "campus". geometry – POLYGON geometry of area footprint (in "campus" and "building" layers) or POINT geometry of locations (in "point" layer). This parameter is not included in the csv download. Attribution Data center locations were derived from OpenStreetMap, which is made available at openstreetmap.org under the Open Database License (ODbL). US state and county boundary information was collected from the US Census Bureau for the year 2024, which is made publicly available at https://www.census.gov/geographies/mapping-files.html Acknowledgment IM3 is a multi-institutional effort led by Pacific Northwest National Laboratory and supported by the U.S. Department of Energy's Office of Science as part of research in MultiSector Dynamics, Earth and Environmental Systems Modeling Program. License The IM3 Open Source Data Center Atlas is made available under the Open Database License: http://opendatacommons.org/licenses/odbl/1.0/. Disclaimer This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor the Contractor, nor any or their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. PACIFIC NORTHWEST NATIONAL LABORATORYoperated byBATTELLEfor theUNITED STATES DEPARTMENT OF ENERGYunder Contract DE-AC05-76RL01830

Mongird, Kendall [Pacific Northwest National Labor↗

IM3 Open Source Data Center Atlas

IM3 Open Source Data Center Atlas Description This dataset contains locations of existing data center facilities in the United States. Data center locations were derived from OpenStreetMap (OSM), a crowd-sourced database. Data points from OSM are processed in various ways to determine additional variables provided in the data including: facility area (square feet), associated US county, and US state. This dataset can be used to identify areas of concentrated data center development and inform government and private sector planning strategies for future buildout of data centers and the infrastructure necessary to support it. Usage Notes Validation of OSM-derived data center locations is an ongoing development under the IM3 project, and the database will be updated as new information becomes available. In some instances, both the data center area (e.g., campus) and individual data center buildings are included as overlapping areas in the database. Both values are retained. Data center points, buildings, and campus areas are provided as separate layers in the downloadable data package. Note that data items are not necessarily complete across layers. That is, a specific data center may only be present as a single point geometry in the "point" layer while other data centers are represented in both the campus and building layers. In some cases, data center campuses and/or buildings straddle a county boundary line. Mappings to both counties are retained in the database as separate rows. These data rows will have the same data center id information, but each will have different county information. Crowd-sourced data, by nature, relies on individuals and communities to provide information. As a result, some data may be missing where it has not yet been reported. As we collect information on additional data center locations and as OSM receives additional contributions, the database will be updated to capture additional data points not yet shown. Data items will occasionally be removed from OSM if they are misidentified, if they no longer exist, if they are duplicates of another item, or similar. For that reason, updated versions of this database may not contain all data center locations included in previous versions. Technical Information Data is available for download under the following formats: GeoPackage (GPKG) CSV Geospatial data is provided in the WGS84 (EPSG:4326) coordinate reference system. The GeoPackage download contains the following layers. See usage notes for more information. "point" "building" "campus" The "point" layer includes all data from OSM that had POINT geometry type (i.e., individual coordinates). The "building" layer includes all OSM data that did not have POINT geometry and where the building tag in the OSM export was neither equal to "no" or null. Data that did not meet the "point" or "building" qualification was assumed to be a facility campus and included in the "campus" layer. The dataset contains the following parameters. Variables provided by OSM are labeled with (OSM-provided). id - unique identification number (OSM-provided with prefix of "node/", "relation/" and similar attributes removed) state - name of US state state_abb - two letter US state abbreviation state_id - state ID number county - name of US county county_id - county ID number ref - reference numbers or codes (OSM-provided) operator - the name of the company, corporation, or person in charge facility (OSM-provided) name - name of facility (OSM-provided) sqft - surface area of facility polygon, measured in square feet. Only available for "building" and "campus" layers lat - latitude of data centroid point lon - longitude of data centroid point type – represented spatial information. One of "point", "building", or "campus". geometry – POLYGON geometry of area footprint (in "campus" and "building" layers) or POINT geometry of locations (in "point" layer). This parameter is not included in the csv download. Attribution Data center locations were derived from OpenStreetMap, which is made available at openstreetmap.org under the Open Database License (ODbL). US state and county boundary information was collected from the US Census Bureau for the year 2024, which is made publicly available at https://www.census.gov/geographies/mapping-files.html Acknowledgment IM3 is a multi-institutional effort led by Pacific Northwest National Laboratory and supported by the U.S. Department of Energy's Office of Science as part of research in MultiSector Dynamics, Earth and Environmental Systems Modeling Program. License The IM3 Open Source Data Center Atlas is made available under the Open Database License: http://opendatacommons.org/licenses/odbl/1.0/. Disclaimer This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor the Contractor, nor any or their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. PACIFIC NORTHWEST NATIONAL LABORATORYoperated byBATTELLEfor theUNITED STATES DEPARTMENT OF ENERGYunder Contract DE-AC05-76RL01830

Mongird, Kendall [Pacific Northwest National Labor↗

The Nasa SRA Process as It Relates to Open-Source Workflows Developed for GeneLab Data Processing

To release open, standards-compliant processed data sets in the Open Science Data Repository (OSDR), the GeneLab Data Processing team works with the scientific community through the OSDR Analysis Working Groups to design and build open-source data processing pipelines. Once baselined internally, these pipelines are wrapped into workflows and published on the NASA GeneLab Data Processing public GitHub repository along with detailed instructions for installation and use. Each workflow must be approved through NASA's Software Release Authorization (SRA) process prior to publishing. However, the SRA process lacks sufficient documentation and clarity regarding which forms are applicable for new open-source software that utilizes publicly available 3rd party tools, and the SRA process can take several months to complete, making sharing software outside of NASA cumbersome and in contradiction with the concept of Open Science. Furthermore, the SRA process was designed as a one-size fits all approach and thus many of the questions asked are not applicable to our open-source workflows. Here we describe the software provided on the NASA GeneLab Data Processing GitHub repository, summarize our experiences with the SRA process to release these software, and propose a more stream-lined approach for review of open-source projects.

Software Release Authorization↗

The NASA SRA Process as it Relates to Open-Source Workflows Developed for GeneLab Data Processing

To release open, standards-compliant processed data sets in the Open Science Data Repository (OSDR), the GeneLab Data Processing team works with the scientific community through the OSDR Analysis Working Groups to design and build open-source data processing pipelines. Once baselined internally, these pipelines are wrapped into workflows and published on the NASA GeneLab Data Processing public GitHub repository along with detailed instructions for installation and use. Each workflow must be approved through NASA's Software Release Authorization (SRA) process prior to publishing. However, the SRA process lacks sufficient documentation and clarity regarding which forms are applicable for new open-source software that utilizes publicly available 3rd party tools, and the SRA process can take several months to complete, making sharing software outside of NASA cumbersome and in contradiction with the concept of Open Science. Furthermore, the SRA process was designed as a one-size fits all approach and thus many of the questions asked are not applicable to our open-source workflows. Here we describe the software provided on the NASA GeneLab Data Processing GitHub repository, summarize our experiences with the SRA process to release these software, and propose a more stream-lined approach for review of open-source projects.

Software Release Authorization↗

The case for free and open source software in research and scholarship

Free and open source software (FOSS) is any computer program released under a licence that grants users rights to run the program for any purpose, to study it, to modify it, and to redistribute it in original or modified form. Here, our aim is to explore the intersection between FOSS and computational reproducibility. We begin by situating FOSS in relation to other ‘open’ initiatives, and specifically open science, open research, and open scholarship. In this context, we argue that anyone who actively contributes to the research process today is a computational researcher, in that they use computers to manage and store information. We then provide a primer to FOSS suitable for anyone concerned with research quality and sustainability—including researchers in any field, as well as support staff, administrators, publishers, funders, and so on. Next, we illustrate how the notions introduced in the primer apply to resources for scientific computing, with reference to the GNU Scientific Library as a case study. We conclude by discussing why the common interpretation of ‘open source’ as ‘open code’ is misplaced, and we use this example to articulate the role of FOSS in research and scholarship today.

97 MATHEMATICS AND COMPUTING↗

Developing an Open Source Option for NASA Software

We present arguments in favor of developing an Open Source option for NASA software; in particular we discuss how Open Source is compatible with NASA's mission. We compare and contrast several of the leading Open Source licenses, and propose one - the Mozilla license - for use by NASA. We also address some of the related issues for NASA with respect to Open Source. In particular, we discuss some of the elements in the External Release of NASA Software document (NPG 2210.1A) that will likely have to be changed in order to make Open Source a reality withm the agency.

Moran, Patrick J.↗

LiAISON (Life-cycle Assessment Integration into Scalable Open-source Numerical models) [SWR-24-01]

We introduce an open source prospective LCA framework, the Life-cycle Assessment Integration into Scalable Open-source Numerical models (LiAISON), to analyze the non-linear relationships between technology foreground and the future energy system background across a series of midpoint and resource use metrics The integration of LCA and IAM data is achieved using prospective environmental Impact assessment (PREMISE)7. We showcase it by assessing two Power-to-Hydrogen (PtH2) processes, namely Solid Oxide Electrolysis (SOE) and Polymer Electrolyte Membrane Electrolysis (PEME). We compare the technologies to a baseline of hydrogen production via natural gas-based Steam Methane Reforming (SMR) in a US context of multiple energy system and climate change mitigation futures. Besides providing an analysis that specifies the LCA results ranges with temporal and geospatial explicitness across the two technologies, metrics, and impact assessment methods, this research also aims to establish a base framework that can be expanded to use other IAM generated scenarios and US open-source life cycle inventory (LCI) databases. We find that the temporal environmental performance of either technology or their difference to SMR is directly influenced by the underlying background dynamics. Under baseline projections (i.e., no decarbonization goals), neither process reaches parity with the incumbent technology across several environmental metrics. Under the decarbonization scenarios, the underlying sectoral shifts result in declining impacts over time, compared to 2020 levels, except for metal depletion levels, which increase. The background shifts postulate a heavily decarbonized economy and energy system, which help technologies reach parity with SMR between 2040-2050 (RCP2.6) and 2030-2040 (RCP1.9) for global warming. Despite declines across several other metrics over time, neither PtH2 technology break even with SMR by 2100 besides for global warming. Scientific publication available here: https://pubs.acs.org/doi/full/10.1021/acs.est.2c04246

Ghosh, Tapajyoti↗

TRITON: A Multi-GPU open source 2D hydrodynamic flood model

A new open source multi-GPU 2D flood model called TRITON is presented in this work. The model solves the 2D shallow water equations with source terms using a time-explicit first order upwind scheme based on an Augmented Roe's solver that incorporates a careful estimation of bed strengths and a local implicit formulation of friction terms. Here, the scheme is demonstrated to be first order accurate, robust and able to solve for flows under various conditions. TRITON is implemented such that the model effectively utilizes heterogeneous architectures, from single to multiple CPUs and GPUs. Different test cases are shown to illustrate the capabilities and performance of the model, showing promising runtimes for large spatial and temporal scales when leveraging the computer power of GPUs. Under this hardware configuration, communication and input/output subroutines may impact the scalability. The code is developed under an open source license and can be freely downloaded in https://code.ornl.gov/hydro/triton.

2D flood model↗

Invited: Bambu: an Open-Source Research Framework for the High-Level Synthesis of Complex Applications

This paper presents the open-source High-Level Synthesis research framework Bambu. The framework provides an open-source starting point to experiment with new ideas across High-Level Synthesis, high-level verification and debugging, FPGA/ASIC design, design flow space exploration, and parallel hardware accelerator design. The tool accepts as input standard C/C++ specifications and compiler intermediate representations (IRs) coming from the well-known Clang/LLVM and GCC com- pilers. The broad spectrum and flexibility of input formats allow the electronic design automation (EDA) research community to explore and integrate new transformations and optimizations. The easily extendable modular framework already includes many op- timizations and HLS benchmarks. The integration with synthesis and verification backends (commercial and open-source) allows researchers to quickly test any new finding and easily obtain performance and resource usage metrics for a given application. Different FPGA devices are supported from several different vendors: AMD/XILINX, Intel/Altera, Lattice Semiconductor, and NanoXplore. Finally, integration with the OpenRoad open-source end-to-end silicon compiler perfectly fits with the recent push towards open-source EDA.

Ferrandi, Fabrizio↗

An Evolving Worldview: Making Open Source Easy

NASA Worldview is an interactive interface for browsing full-resolution, global satellite imagery. Worldview supports an open data policy so that academia, private industries and the general public can use NASA's satellite data to address Earth science related issues. Worldview was open sourced in 2014. By shifting to an open source approach, the Worldview application has evolved to better serve end-users. Project developers are able to have discussions with end-users and community developers to understand issues and develop new features. New developers are able to track upcoming features, collaborate on them and make their own contributions. Getting new developers to contribute to the project has been one of the most important and difficult aspects of open sourcing Worldview. A focus has been made on making the installation of Worldview simple to reduce the initial learning curve and make contributing code easy. One way we have addressed this is through a simplified setup process. Our setup documentation includes a set of prerequisites and a set of straight forward commands to clone, configure, install and run. This presentation will emphasis our focus to simplify and standardize Worldview's open source code so more people are able to contribute. The more people who contribute, the better the application will become over time.

open dat↗