Open Research Devroom
A place to discuss the creation and use of Free Libre Open Source Software in research context: science, investigative journalism, activism, OSINT...
2024 Open Research Online Devroom talks
Date and time: Saturday the 10th of February at 10:00 UTC - 15:30 UTC. [Check when this is in YOUR timezone]
The call will be hosted on Zoom, allowing us to provide realtime captions and translation.
Join Zoom Meeting https://us02web.zoom.us/j/84519906281?pwd=UGpuMFBHeis3RTE3c0dnc2c5dUZTZz09
Meeting ID: 845 1990 6281
Passcode: 138837
Interactive Q&A doc: https://annuel2.framapad.org/p/open-research-2024-online
Schedule:
| S/No. | TIME (CET) | End | Title | Author | Chair | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 11:00 | 11:15 | Representing epistemological and disciplinary diversity in open research discourse | Pen-Yuan Hsing, Brianna Johns | Yo | ||||||
| 2 | 11:15 | 11:30 | MolerHealth: An Open Source Electronic Health Record System | Monsurat Onabajo | Yo | ||||||
| 3 | 11:30 | 11:45 | The Ersilia Model Hub, a FOSS platform for antimicrobial drug discovery | Emmanuel Onwuegbusi | Yo | ||||||
| 4 | 12:00 | 12:30 | Caring for Gephi - What care for a FLOSS project entails | Mathieu Jacomy | Yo | ||||||
| 5 | 12:30 | 13:00 | Break | ||||||||
| 6 | 13:00 | 13:15 | An integrated Knowledge Management System to support Open Science training | Deborah Udoh | Mathieu | ||||||
| 7 | 13:15 | 13:30 | Sustainable Agricultural Practices and Climate Mitigation through Digitalization in Nigeria | Gloria Ashiegbu | Mathieu | ||||||
| 8 | 13:30 | 13:45 | Discussion | ||||||||
| 9 | 13:45 | 14:15 | Empowering Citizens: Unveiling the ‘Querido Diário’ Platform for Accessing Brazilian City Policies | José Guilherme Vanz | Mathieu | ||||||
| 10 | 14:15 | 14:30 | Fostering Diversity and Sustainability in the Open Source Scientific Software Community: The rOpenSci Champions Program | Yanina Bellini Saibene | Sara | ||||||
| 11 | 14:30 | 14:45 | Analizo, 15 years of a multi-language Research Software tool for source code analysis | Joenio M Costa | Sara | ||||||
| 12 | 14:45 | 15:00 | Discussion | Sara | |||||||
| 13 | 15:00 | 15:30 | From the Inside Out: Organizational Impact on Open-Source Communities and Women’s Representation | Hana Frluckaj | Sara | ||||||
| 14 | 15:30 | 16:00 | Panel | organisers discussion panel |
Abstract of Talks
MolerHealth: An Open Source Electronic Health Record System
Abstract: In Nigeria, Many healthcare institutions rely on traditional, paper-based methods. This fragmented approach often means that when patients move or visit a different hospital, their comprehensive health history isn’t readily available and In critical situations, this lack of immediate access to previous health records can have severe implications, including misdiagnosis or delayed treatments, sometimes even resulting in avoidable loss of life. Our project, MolerHealth, aims to address this significant gap. We’re developing a centralized platform to store these vital health records. The vision is for this platform to serve as a comprehensive repository accessible by both hospitals and individual patients.This innovative web application not only consolidates patient data but also utilizes machine learning and artificial intelligence, to anticipate potential health issues. By providing early warnings and data-driven recommendations, MolerHealth enables both patients and healthcare providers to take proactive steps in healthcare management. As an open-source platform, MolerHealth encourages community participation, allowing for continuous improvement and adaptation to the specific healthcare needs of various regions within Nigeria. This approach promises to enhance healthcare efficiency and facilitate more informed decision-making, potentially mitigating the health crises caused by inadequate data management.
Description: The Molerhealth project is an initiative aimed at transforming healthcare in Nigeria through the development of an open-source electronic health records (EHR) application. The goal is to address the critical issue of disease misdiagnosis by enabling better information sharing and collaboration between healthcare providers, leading to improved patient outcomes and a more efficient healthcare system. Molerhealth will provide individuals with a secure and user-friendly platform to access, update, and share their comprehensive health records, regardless of their location or healthcare provider. Through this comprehensive EHR system, patients will have seamless continuity of care, as their medical history, test results,medications, allergies and treatment plans will be readily available to healthcare professionals. By harnessing the power of technology, Molerhealth will significantly reduce the rate of misdiagnoses in Nigeria. Doctors will have access to a complete and up-to-date patient profile, enabling accurate diagnoses, appropriate treatment decisions, and timely referrals to specialists when necessary. Moreover, Molerhealth will facilitate better communication between healthcare providers by providing a platform for secure messaging and consultation, enabling the exchange of vital patient information. This collaboration will lead to more informed decision-making, increased efficiency, and ultimately, improved healthcare outcomes. Through its open-source nature, Molerhealth will encourage community participation, innovation, and customization, making it adaptable to the unique healthcare needs of different regions in Nigeria. It will,serve as a catalyst for positive change, empowering individuals, and strengthening the healthcare ecosystem as a whole. Talk License: While our web application’s code is open source and is licensed under the MIT License, the data it processes is rigorously protected and not subject to open-source sharing in order to ensure strict confidentiality and safeguard user privacy.
Speaker Name: Monsurat Onabajo. Biography: Monsurat, hailing from Nigeria, is a dedicated data scientist and open source advocate with a passion for leveraging technology to advance the healthcare systems of her country and the African continent at large. Her focus lies in using open source projects to bring about significant improvements in healthcare delivery and outcomes across Africa. Others: To know more about molerhealth, Please see here: https://github.com/MolerHealth/MolerHealth-Documentation
The Ersilia Model Hub, a FOSS platform for antimicrobial drug discovery.
Abstract: The Ersilia Model Hub serves as a free, open-source repository housing Artificial Intelligence and Machine Learning (AI/ML) models tailored for drug discovery. Its primary objective is to assist researchers in identifying potential drug candidates for orphan and neglected diseases, facilitating de novo molecule design, comprehending mechanisms of action, and predicting adverse side effects. Ersilia aims to establish itself as the go-to reference resource for AI/ML models in biomedical research, particularly emphasizing drug discovery for infectious and neglected tropical diseases that disproportionately impact the Global South. The ultimate mission is to reduce barriers to drug discovery, fostering the engagement of both academic groups and companies in developing new medicines while adhering to the principles of open science. In this talk, we will also discuss how we have built a global community of researchers, code contributors, and volunteers from the industry, non-profit and academic sectors, and underrepresented minorities in STEM to, collectively, build open source software that will contribute to ending infectious disease threats.
Description: After the talk, attendees will understand what the Ersilia Model Hub and Ersilia itself are about and how it is helping reduce the barriers to drug discovery, fostering the engagement of both academic groups and companies in developing new medicines while adhering to the principles of open science. Talk license: Our code is licensed under a GPLv3 License and the content and materials of the talk will be licensed under a CC-BY-4.0 Attribution-ShareAlike License.
Speaker: Name: Emmanuel Onwuegbusi; Biography: Research software engineer and open source contributor (former Outreachy intern) to Ersilia. Availability: Any hour on Saturday, 10th Feb 2024. Submission notes: Lightning Talk (15 minutes). Extra review material: Ersilia’s CodeBase: https://github.com/ersilia-os/ersilia; Ersilia’s Documentation: https://ersilia.gitbook.io/ersilia-book; Organisation’s Website: https://ersilia.io
Caring for Gephi
Abstract: I’ve been caring for Gephi, an open source network software I co-created and keep contributing to.
This talk draws on a book about maintenance called “Le Soin des Choses” (the care of things) by Jérôme Denis and David Pontille (in French, to be published in English in 2024). The book is not at all about software, and yet it describes situations that I can relate to, and so could many tool maintainers. This talk is for them.
In short, the points I want to make are the following.
- Maintenance is not like repair in that it does not make an event. This is key to why maintenance is mostly invisible. It does not work well with heroic narratives.
- Maintaining software entails a certain kind of diplomacy, like curating code dependencies. Making compromises is inherent to maintaining. A well-maintained tool is not one that never fails, but one that allows itself to be maintained.
- The software maintainer has to cultivate a proximity to both the users and the technologies. Attention to fragility is at the heart of the maintenance’s mission of preventing failure.
- Maintenance is not a control operation conducted on the basis of stable criteria. Maintaining sometimes deeply transforms, or obliges to transform. There is an ontological share to maintenance. Maintaining changes the maintained tool.
I will provide examples from maintaining Gephi.
Talk licence: CC-BY (https://creativecommons.org/licenses/by/4.0/).
Biography: Mathieu Jacomy is Doctor of Techno-Anthropology and assistant professor at the Aalborg University Tantlab, and MASSHINE center. He was a research engineer for 10 years at the Sciences Po médialab in Paris, and is a co-founder of Gephi, a popular network visualization tool. He develops digital instruments involving data visualization and network analysis for the social science and humanities. His current research focuses on visual network analysis, digital controversy mapping, and computational social science. He toots at @jacomyma@mas.to and blogs at reticular.hypotheses.org.
An integrated Knowledge Management System to support Open Science training.
Abstract: OLS is a non-profit organisation dedicated to capacity building and diversifying leadership in research worldwide (https://openlifesci.org/). Since 2020, we have trained 380+ participants across 50+ countries in Open Science practices, with the help of 300+ mentors and experts. The intentional design of our collaborative processes has allowed us to sustain this growth as a young organisation. In this talk we present our Knowledge Management System (KMS), which reflects our transparent and collaborative approach to knowledge management (https://openlifesci.org/knowledge_management.html). The KMS integrates tools and processes into a structured workflow for the management of information related to various OLS initiatives, community members, partnerships and more. The system uses an open technology stack based on Python scripts and libraries maintained on GitHub, and it links tools like CiviCRM, GitHub Actions, CSV files, Zotero, and Jupyter Notebooks to store and propagate data, display information in our websites and automate tasks. This talk will provide an overview of the KMS’s technical functionalities and highlight how it forms the backbone of our organisational processes, supporting our cohort coordination, keeping track of key impact indicators and facilitating volunteer contributions. We will demonstrate how the KMS can be a useful resource for organisations looking to implement a similar infrastructure.
Talk licence: CC-BY (https://creativecommons.org/licenses/by/4.0/).
Speaker name, contact, biography: Name: Deborah Udoh. Contact: NPDebs on GitHub. Bio: Debs is OLS’s web developer and also a registered nurse in Nigeria. A spirited human with a passion for collaboration, she derives immense satisfaction from contributing to open-source projects. She is on a journey to discovering the place between healthcare and tech where she fits in, while breaking some stereotypes along the way. When not caring for beautiful humans, creating pull requests or resolving bugs, you can find her immersed in the world of podcasts and horror flicks. Fun fact: In my head, I am mother to 7 cats. Submission notes: This is a submission for an Online lightning talk. Additional speakers: • Bérénice Batut • Irene Ramos
Sustainable Agricultural Practices and Climate Mitigation through Digitalization in Nigeria.
Ashiegbu G.N., Adesope O.M., Onunkwo D.N. and Onwumere J.C. ABSTRACT: The field of digital agriculture, which uses a variety of instruments and management techniques, has made significant strides recently with the goal of lowering food insecurity and mitigating climate risk. This talk presents our experience designing a workshop on digital agriculture for youth in Nigeria. The workshop focuses on addressing the intersection of Agriculture, Sustainability, and Climate Change. It aims to provide innovative solutions by leveraging digital technologies to promote sustainable agricultural practices, boost resilience, and actively contribute to climate change mitigation. Agriculture is not only a fundamental component of global food security but also a significant contributor to greenhouse gas emissions. The workshop emphasizes the formation of communities, collaboration, and partnerships, while also delving into the effective management of farm data through open sources. Central to the discussion is building trust within communities through transparent open data sharing practices. Gaining community trust through open data sharing involves establishing Transparency, accountability, ensuring that the data shared is valuable, accurateand accessible. The key principles and strategies to build trust in the community through open data sharing are having clear purpose and goals, Data quality assurance, privacy protection, Open communication channels, User-friendly access, Open data policies access, Gender inclusiveness, Advisory community.
Talk licence: CC-BY https://creativecommons.org/licenses/by/4.0/. Talk format: a lecture talk (25 min).
Speaker name, contact and short biography: ASHIEGBU GLORIA NWAKAEGO. MICHAEL OKPARA UNIVERSITY OF AGRICULTURE UMUDIKE ABIA STATE, NIGERIA. Biography: I, Ashiegbu Gloria N. have been involved in participatory research in agricultural and rural development. My areas of interests includes rural development, agricultural education, Information and Communication Technologies in Agriculture. I have practical experience with community women organizations and youth in community based organizations(CBOs) and non-governmental organizations where I have been involved in enterprise development for women. I am a lecturer at the Michael Okpara University of Agriculture Umudike Abia State, Nigeria and currently a Ph.D research student at the Universiti Putra Malaysia.
Empowering Citizens: Unveiling the ‘Querido Diário’ Platform for Accessing Brazilian City Policies.
Abstract: In an era dominated by digital advancements, numerous Brazilian cities still adhere to outdated publication practices for local policies and decisions, resulting in information being ensnared within unstructured and inaccessible documents. This poses a significant obstacle for individuals seeking to comprehend and track policymakers’ decisions. Enter “Querido Diário” – a project designed to revolutionize the landscape. The Querido Diário initiative is dedicated to meticulously mapping, extracting, indexing, and processing this wealth of information, rendering it accessible through a user-friendly interface and API. These resources enable users to effortlessly search for information or develop their own applications. This presentation will delve into the intricacies of our approach, offering insights into the architecture and tools carefully chosen to address this pervasive issue. Join us on a journey uncovering how “Querido Diário” is breaking down barriers and empowering citizens to engage with their city’s policies in a meaningful way. Notes: https://queridodiario.ok.org.br/, https://github.com/okfn-brasil/querido-diario-data-processing, https://github.com/okfn-brasil/querido-diario/blob/main/docs/README-en-US.md.
Talk licences: Creative Commons licences. Speakers: José Guilherme Vanz, bio: Just a guy fixing and creating bug worldwide. Currently working for SUSE and helping OKFN Brazil building the Querido Diário platform; Giulio Carvalho, bio: Since 2020, Giulio has been a mantainer for the “Querido Diário” project and also part of the network of Civic Innovation Ambassadors at Open Knowledge Brazil (OKBR). Currently, he serves as the Civic Innovation Program Manager at OKBR. He is also an active Python community member since 2017, presenting talks, organizing events and helping others grow together with the community.
Fostering Diversity and Sustainability in the Open Source Scientific Software Community: The rOpenSci Champions Program.
Abstract: Research software plays a crucial role in advancing knowledge and innovation, and its development should be inclusive and representative of the diverse communities it serves. Unfortunately, the R and research software communities face a lack of diversity, with developers predominantly being white, male, and from a limited number of countries. This lack of inclusivity raises concerns about the long-term sustainability and utility of projects. In response to this challenge, the rOpenSci Champions Program specifically targets individuals from underrepresented groups who are keen on contributing to rOpenSci and the broader open science ecosystem. In this talk, we will share the motivations behind the creation of the rOpenSci Champions Program, exploring its goals, structure, and the opportunities it provides for participants. We will share insights gained from the implementation of the program’s pilot phase, highlighting key outcomes, success stories, and lessons learned. Attendees will gain a deeper understanding of the strategies employed to foster a more inclusive and diverse developer community in the R ecosystem. By showcasing the rOpenSci Champions Program, this talk aims to inspire similar initiatives across the open source landscape and contribute to the ongoing dialogue on enhancing diversity, sustainability, and collaboration in research software development. Talk license:CC-BY.
Speaker name: Yanina Bellini Saibene. Biography: Yani is an Argentinean researcher, undergraduate and graduate professor at several universities in Argentina and Uruguay. She has developed open courses and tutorials to teach technical skills in data science, and leads and participates in the community translation of educational and technical material into Spanish. She is also the Community Manager of rOpenSci and one of the co-founders of LatinR. She is a trainer, instructor and member of the Board of Directors of The Carpentries and a certified Posit instructor. She is a member of the R Consortium Infrastructure Steering Committee and the Sociedad Argentina de Informática (SADIO). She is R-Ladies Global Project Lead and part of their Board of Directors.
From the Inside Out: Organizational Impact on Open-Source Communities and Women’s Representation
Abstract: The involvement of companies and public institutions in open-source software (OSS) has become widespread. While studies have explored the business models of for-profit organizations and their impact on software quality, little is known about their influence on OSS communities, especially in terms of diversity and inclusion. This knowledge gap is significant, considering that many organizations have the resources to enhance diversity and inclusion internally, but whether these efforts extend to OSS remains uncertain. To address this gap, we conducted interviews with maintainers of community-owned and organization-owned OSS projects, revealing tensions between organizations and their projects and identifying the impact of internal policies on OSS communities. Our findings offer insights into how organizations can contribute to improving diversity and inclusion in their open-source projects and, consequently, in the wider open-source community.
Description: This talk will convey the findings of an upcoming paper on the influence of organizational structure on OSS projects and their contributor diversity. We found that internal organizational practices and policies can shape the level and nature of community engagement and influence project contributor diversity. We consider how organizations can leverage internal resources to cultivate a more diverse and inclusive open-source community. By addressing barriers to external contributors, building external communities, promoting mentorship programs, and fostering open discussions on community-oriented efforts, organizations can contribute to a more inclusive open-source ecosystem. Our findings highlight the importance of organizational involvement and proactive measures in shaping the diversity and inclusivity of open-source projects. Further research on open-source governance models and the implementation of these strategies will be valuable in promoting a more inclusive and accessible open-source community for all.
Talk License: MIT license. Speaker Info: Hana Frluckaj, PhD student at UT-Austin iSchool, flexible availability.