Andrew West (CC BY-NC-SA 2.0)
Participants join this program with a project that they either are already working on or want to develop during this program.
By: Zarena Syrgak
Keywords: equity, diversity, inclusion, open scholarship, multilingual open science, epistemic/linguistic, justice
The project Multilingual Open Science aims to create an open educational resource about FAIR research in Central Asian (CA) languages. The goal is to popularise and raise local researchers’ awareness of open science practices and platforms and thus to tackle the existing structural barriers (e.g., linguistic, epistemic, etc.) in accessing the information and disseminating the research from Central Asia. Currently, the local scholarship is located - geographically, linguistically, epistemically - in the global periphery which hinders the knowledge production, use, and dissemination in the region. Many scholars, as the result, become trapped in fraudulent research and publication practices. Moreover, there are cases when openly accessible educational resources are offered to researchers as a marketable product. So, to address these and other issues related to inaccessibility of knowledge production infrastructure, this project aims to create an openly accessible, fair, and multilingual educational resource about open science with the particular focus on Central Asia. To this end, I am planning to use Jupyter Notebook and create a platform similar to The Turing Way.
Mentored by: Alexander Martinez Mendez
Keywords: training and education, research community, editorial community, open journals systems.
Our initiative is called “Training Latin American scientists community to create high-quality open journals with good editorial standards”. We intend to build a community of native spanish speaking scientists who teach and learn about creating editorial boards and open access scientific journals that meet international high editorial quality standards. We intend to organise hands-on workshops about different steps in the editorial process of creating scientific open access journals, with experienced trainers and with open source tools. Some of the topics we would like to cover are:
These workshops would merge synchronic and asynchronic activities throughout a period of 6 weeks, so that trainees get to learn all the necessary concepts through, familiarize with the required software and conceptualize and brainstorm solutions to the local needs for the journals they intend to develop, with peer support and mentoring.
By: Evelyn Greeves
Mentored by: Anne Fouilloux
Keywords: Education, Training, Environmental biotechnology, Omics, Community
Cloud-SPAN trains researchers, and the research software engineers that support them, to run specialised analyses for environmental omics datasets on cloud-based high-performance computing infrastructure. It is a collaboration between the University of York and The Software Sustainability Institute funded by the UKRI Innovation Scholars award (Project Reference: MR/V038680/1). The primary objective of the project is to generate training materials and opportunities which are open, accessible and reusable (FAIR) for all researchers. We aim to build an engaged community of practice around the participation in, and the development and maintenance of, the materials. The community-building element would be the main focus of the OLS scheme project.
By: Sitsofe Morgah
Mentored by: Anne Treasure
Keywords: Sustainabilty, Open science, Carbon footprint, Buildings
There is a considerable gap in cases of sub-Saharan African countries regarding assessment of embodied energy of building materials and operational energy of various building types. Lack of data remains a critical barrier to closing this gap. Creating a database of embodied energy of building materials and operational energy of building typologies will be key in establishing the carbon footprint of buildings in Ghana. The development of an online platform will also allow interested groups, individuals and cooperation’s to submit key information needed for the computation of energy outputs in buildings. The aim of this project is to explore the scope and path towards establishing an open database and an inclusive community.
Keywords: open publishing, open access, open peer review, scholarly communication
TU Delft OPEN Publishing, Open Access academic publisher of the TU Delft, publishes open access (OA) journals and open (text)-books. The OA journals currently receive not enough support regarding their development. This project aims to bring all OA journals to the same high level of quality expected of any TU Delft product. This project will establish the identity of TU Delft OPEN Publishing as a trustworthy academic publisher within and beyond TU Delft. The success of the plan is linked to the open collaboration of the journal editorial boards. The publishing plan will help journals
The plan needs to integrate as much as possible open science principles such as Open Data, Open peer review or authorship transparency in their publishing processes. While the plan will benefit all, It should consider the specificity of each journal. Overall the plan has to demonstrate its value to the editorial board.
By: Biandri Joubert
Mentored by: Batool Almarzouq
Keywords: Rstudio, qualitative research, quantitative research, legal research, law
This project is envisioned as one that ends up as something that can explain the “why” when encouraging people from legal backgrounds to learn R and some data science. A case for open and reproducible research in a field that does not typically use R and qualitative methods. The idea is to get to that point by creating different data sets derived from commonly used legal sources that law students or graduates would be familiar with and incorporating them into a single platform with a few examples of practical use and application as well as code to encourage such persons to see the “why”. On this platform, I would like to share resources to places where the intro to R courses are available, etc. At this stage, this is an idea I have and I hope to develop it as the week’s progress.
Keywords: Next-generation sequencing, data analysis, bioinformatics, genomics, open education, open resource
Next-generation sequencing (NGS) is a revolutionary technique with wide applications in biology. Its applications are widely being used from young researchers to pioneer researchers of the field. The NGS data analysis has various approaches and many resources are explaining these methods. However, it can be difficult for beginners in this field to quickly understand and apply these methods. Also, beginner researchers might not have enough knowledge to overcome the most common errors that are encountered during these analyses. Due to the challenges that we mentioned above, in this project, we aimed to create a comprehensive open educational resource explaining NGS data analysis and its different methods and offer an example for the application of methodology and solutions to the most common errors. We believe that this project will be enlightening for anyone interested in NGS data analysis by providing a necessary roadmap.
By: Sarah Nietopski
Mentored by: Caleb Kibet
Keywords: community, community engagement, open learning, Data Science and AI education, training
This project aims to establish and nurture an active (virtual) community of learners with the Turing. The Institute is in the process of creating an open online learning platform to host training and learning materials, covering a range of subjects related to Data Science and AI. In order to ensure that the offering is useful to our audience, that it is responsive to their needs, and that it continues to grow, it is key to involve them in the creation and direction of the resources. Having real user voices and input will help to create an open learning space that is truly useful and valuable. Not only that, but the platform can serve as a central meeting point where learners can come together over shared interests and issues, and collaborate on projects that may have a wider impact. In order to do this, learners will need a way to connect and communicate effectively.
By: Kim Martin
Mentored by: Deepak Unni
Keywords: forestry, xylogenesis, wood formation, ecophysiology, FAIR, metadata, models, data, ontologies, knowledge graph
This project aims to assist researchers in the field of wood formation and ecophysiology to explore datasets and computational models in a flexible and integrative way. The goal is to provide a platform - in the form of an open knowledge graph and associated interface - that will allow researchers (even those with minimal familiarity with the underlying technology) to explore linked representations of metadata for the included datasets and models. Researchers should be able to survey a variety of models that target phenomena at different scales; ranging from process-based models of the cellular determinants of wood formation, to empirical models of gross tree growth in different environmental contexts. The linked information should allow complex questions to be asked, including: how similar models differ; which datasets can be repurposed to test different model outputs; and identifying whether and how different models can be composed together. This will promote open scientific practices in this research area (through the use of common metadata standards and terms), and may serve as a valuable framework for collaborative knowledge capture and exploration.
Mentored by: Diego Onna
Keywords: DIY Bio, Open Source, Biohacking, Computational Biology, Python programming, R programming
We propose SciHack, as the first Open Community Lab in Peru. Our principal aim is to make available the tools and resources necessary for anyone, including non-professionals, to conduct biological engineering research and learning. As part of our activities, we will focus on democratizing science and biotechnology knowledge in low-income populations of Peru where there’s little to no presence of science and technology education. To address these issues, we will conduct workshops about DIY lab equipment, Bioinformatics open source projects and educational resources, and molecular biology tools to train teachers and teach students how to make and analyze scientific experiments. Furthermore, by the end of our activities, we would like to implement a space for bio-makers of all ages and backgrounds to conduct research projects and build prototypes. In this way, we would be fighting against misinformation of science methodology and results that are primordial not only for the current COVID19 situation but also for the progress of science.
Mentored by: Emmy Tsang
Keywords: peer-mentoring, open source, collaboration, academic, Turing Way, ethics, communication
I would like to work with the Skills Team at the Alan Turing institute in order to create a peer-mentoring training programme from the main topics of The Turing Way. Our aim is to turn the five main areas in The Turing Way, namely research reproducibility, project design, collaboration, communication, and ethics into modules which the participants of the peer-mentoring programme can work on together. They would apply it on their own research/ projects, therefore they could put the learnt knowledge in use immediately. The aim of The Turing Way has been to be an open source, collaborative, applicable, and practical tool, and with this programme we would like to facilitate the use of it. We would like to see how people in their different stages of their career (PhD, Post-Doc, Researcher, Admin) can collaborate to deepen their knowledge about the contents of The Turing Way, while understand each other’s perspective on the subject. If the prototype is successful, we would like open it up for any applicants interested in applying the practices of The Turing Way to their own projects as part of the other trainings offered by the Institute.
Mentored by: Esther Plomp
Keywords: software, homogeneous catalysis, data-driven chemistry, chemical space, transition, metal complexes, open-source
Together with co-workers, I have developed a Python-based tool (Source code, publication 1, publication 2) which can be used to explore the local chemical space of an existing molecular scaffold. Homogeneous catalysts are important in many of our daily processes, but also in our fight against climate change. Our goal was to create a tool that can automatically generate large datasets that can be used in research for data-driven catalyst discovery.
The issue was that a simple SMILES representation of a molecular scaffold does not work when it contains a transition metal complex. With this tool we use the 3D coordinates of a molecular scaffold and let the user place molecular fragments to create many variations of this scaffold. Other inorganic chemistry fields that use transition-metal containing molecules might benefit from this tool as well. A first prototype is published, but several things can be done to increase the usability of our tool.
By: Gemma Turon
Mentored by: Fotis Psomopoulos
Keywords: reproducibility, sustainability, accessibility, artificial intelligence, community engagement
We have created the Ersilia Model Hub, a FLOSS platform containing AI/ML models for infectious and neglected disease research . These models can be accessed with little to no-coding expertise, solving a major roadblock in the applicability of such technologies to day-to-day research. The Hub currently includes a hundred open source models, both from the literature and developed by the Ersilia organization. With this project, we aim to open the Hub to the whole computer science community, encouraging third-author model depositions so that the code they develop is not simply open source but also deployed in a user-friendly manner. By leveraging the Hub architecture, computer scientists can reach more users, interact with them and further the impact of the assets they have developed by facilitating its implementation in real case scenarios. To this end, the project will focus on establishing clear guidelines on the quality of the software and its reproducibility (as it won’t necessarily be yet peer-reviewed) and creating a standard model deposition form and minimum required documentation. The ultimate goal of the project is to build a community of contributors by facilitating their access.
By: Robert Schreiber
Keywords: free resources, autism, translation
Living in South Africa, and in much of the world, you can see a large gap in the accessibility of healthcare resources based on a person’s income and education level. I am privileged enough to have had access to good quality healthcare resources throughout my life, which resulted in me being seen by numerous different therapists, counsellors and psychologists and being diagnosed with Autism Spectrum Disorder, more specifically Asperger’s syndrome. I am also privileged in that I am able to comfortably speak and read English. Unfortunately, a large percentage of our country has a very poor level of education, often not being able to read or speak English very well. Most South African resources I have found for individuals with, and parents of children with, autism are only available in English. My project aims to create a database of resources in a variety of South African languages, both written and as a video format (due to poor literacy rates, especially among older generations due to historical discrimination), in easy to understand language and with concepts that are easy to grasp. This is also useful as more people will be able to access online resources than resources at a healthcare facility.
Keywords: Open Source, Community, Governance, Research
As open science projects mature, they attract, engage and retain members who actively participate and contribute to the project. They build Communities of Practice around the project through knowledge exchange, maintenance or development practices and ultimately guide the future directions for both the projects and their communities. To build a more equitable, resilient and sustainable open infrastructure for a diverse community, it is important to select governance models that give voices to people (users, contributors and wider society) from different socio-technical and socio-cultural backgrounds, identities, career stages, contextual needs and research communities. The Turing Way is a guide for reproducible, ethical and collaborative research and data science. Open Life Science is a training and mentoring program to help researchers learn and apply open principles in their work. They are mission-aligned open science projects that involve participants from around the world to create something deeply meaningful for them. The Turing Way has grown exponentially in the last three years that offers more than 200 pages co-created by more than 300 contributors. Open Life Science has offered 4 cohorts in the last 2 years and currently supports a community of over 300 members (present and past mentees, mentors and experts). To support the governance work in these projects in 2022, I would like to carry out a systematic study of governance models suitable for decentralised and distributed communities such as these. By creating a portfolio of governance models suitable for projects at different maturity levels, members from these projects will be able to identify the right model for their respective projects. The aim is to establish norms, workflows and processes that ensure a democratic structure for decision-making and leadership in a way that contributes to projects’ own visions while collaborating on the shared mission for global open science.
Keywords: Community Building, Open Science, Open Data, Open Access, Phytolith, Archaeology, Palaeoecology.
The International Committee on Open Phytolith Science (ICOPS) was initiated as a new committee within the International Phytolith Society in September 2021 and the first committee meeting took place in December 2021. This committee aims to increase the knowledge of and implementation of open science practices in phytolith research. We are embracing an open source approach to our work in this committee so that the work of our committee is transparent. This will include open documentation, regularly communicating with our community, and providing guidelines and communication channels to enable our community to engage with us. Therefore, we want to establish a solid base for this work going forward by further developing our GitHub repository - adding clear contributing guidelines and documentation on how the committee is to be run. All members of the committee will also benefit from training in all aspects of open science practices. This will allow us to gain further insight into the training and initiatives that we want to work on with our community. We will also start to develop training packages specific to phytolith research such as in open publishing and open and FAIR data.
By: Vicky Hellon
Mentored by: Katharina Lauer
Keywords: treatment heterogeneity, missing health data, academia-industry partnership, open science
The Turing-Roche strategic partnership was established in June 2021 with the goal of establishing a collaboration in advanced analytics between the two organisations to develop new data science methods to investigate large, complex, clinical and healthcare datasets to better understand how and why patients respond differently to treatment, and how treatment can be improved. As Community Manager for the project I am developing a collaborative and open community between both organisations and beyond. As the partnership is just beginning and is flexible in nature there are opportunities to embed open practices such as open publication, reproducibility, open data, training, co-working as well as establishing networks such as an early career researchers.
By: Eirini Botsari
Mentored by: Lena Karvovskaya
On of my goals from my current position, as a community manager at the open science community Rotterdam, is to engage and include as many as possible; I want to sustain and grow the community. One of my ambitions is curating events and engage public to open discussions around open science. One of the events that I really want to arrange is through art (as a means) to raise awareness around open science practices, and create the floor for an open discussion around open science. It is still a general idea, so I am aware that I still need to go over all the details and I am still not sure what blockages will rise through this journey. But I am really positive and I truly believe that art is open and can act as a mediator towards connection, expression, openness, and understanding.
Mentored by: Lisanna Paladin
Keywords: History of Science, Philosophy of Science, Research Ethics
A History of Research Ethics is a free, online resource for researchers, governance professionals, and even college students to learn about science and ethics, and be inspired to develop practical tools for the assurance of adequately conducted research. A key purpose of A History of Research Ethics is to demonstrate the variety of disciplines and backgrounds that research ethics can draw on. In other words, interdisciplinarity is critical for its success. This means both interdisciplinary contributions and adapting to audiences from diverse fields and sectors. By embracing the collaborative nature of GitHub and OLS’ open science community, I expect to take A History of Research Ethics to its next stage of development.
By: Cavin Mgawe
Mentored by: Luis Pedro Coelho
Keywords: Non invasive diagnostics, molecular kit development, molecular assays, molecular diagnostics, R programming
This study aims to develop a diagnostic LAMP kit that’s sensitive and robust to Plasmodium falciparum from saliva and urine to enhance simple and easy non-invasive molecular testing. The first phase of this study involved target validation, primer, and probe design using open-access tools. Here, a principal component analysis (PCA) of the R/adegenet package (Jombart et al, 2010) and phylogenetic tree (Neighbour-joining) using R/ape package (Paradis et al, 2004) to cluster repeats of the chosen amplification target. These clusters were aligned to generate a consensus sequence for designing primers and probes for establishing the LAMP assay. I have designed an incorporated strand displacement probe using the engineering guideline of Juan et al, 2015 and the open-access Nupack software tool. The assay has and the master mix is being lyophilized for further experimental evaluation.
The sensitivity of this kit will be evaluated on extracted DNA from three sample types: saliva, urine, and clinical blood, with crude samples, lysed using lysis buffer. Correlation generated from these results will inform the best sensitive amplification. Further, a possible decay of the lyophilised master mix will be evaluated for six months to ascertain possible shelf-life.
By: Jyoti Bhogal
Mentored by: Malvika Sharan
Keywords: Community Building, Creating Pathway, Onboarding, modifying Code of Conduct
In October 2021, the RSE Asia Association was launched. This was done to create awareness in the Asia region about the field of Research Software Engineering. The digital infrastructure for the association has been built during the Open Life Science Cohort 4 (OLS-4) program. The webpage is in place, the contact addresses have also been created for communication with people. A small community has also started emerging. It is time that the community can expand. With the expanding community, it is now required that we create well-defined pathways for people to get onboard to the association. This project aims at building such pathways. Also, a basic Code of Conduct is already present on the RSE Asia webpage. It is to be modified to make it more appropriate for the Asian region.
By: Umar Ahmad
Keywords: RNA-Seq, Bladder Cancer, Transcriptomics, Bioinformatics
We are to process bladder cancer RNA-Seq datasets that are publicly available. The co-authors of this manuscript will work on the analysis and apply bioinformatics methods for analysis of this large scale, heterogeneous RNA-sequencing dataset (20 + samples - 3Gb) that will be downloaded from any of the following databases; Genome Atlas (TCGA) database, Genotype-Tissue Expression (GTEx), cBio Cancer GenCancer Genomics Portal (cBioPortal) database and SRA NCBI database (choose any suitable database you are familiar with). The biological questions of particular interest include
Open source software such as R/Bioconductor (DESeq2), Unix/Linux, Python and Jupyter notebook will be mainly used for the analyses.
Mentored by: Meag Doherty
Keywords: Bioinformatics, Students, data analysis
Bioinformatics Secondary School Outreach (BSSO) is an initiative to develop bioinformatics capacity among High school students in Nigeria and this will create early interest in genomics data analysis among the students and equip them with the relevant skills and knowledge in Bioinformatics. Bioinformatics Hub Nigeria will be training these students on how to use Bioinformatics tools and pipelines and this can be achieved by establishing Bioinformatics research clubs in the visited schools to facilitate the trainings. We would be working alongside with other sister organizations to achieve this goal
By: Gareth Jones
Mentored by: Michael Addy
Keywords: Greenhouse gases, repeatable science, data science, data sharing, data analysis, open source
The OpenGHG project is a NERC funded project that aims to be a community platform for greenhouse gas data science. There is currently no central platform for greenhouse gas / atmospheric chemistry researchers to access standardised data / workflows, or easily share and analyse their measurements. Currently our prototype service processes and standardises the raw measurement data taken from sensor networks worldwide (such as the DECC and AGAGE networks), records associated metadata and makes this data searchable. We are currently in the process of adding the ability to process data from other sources, such as satellite and meteorological models.
Keywords: Data Visualization, database, web application
Visualization of participants by their countries I would like to work on a project ‘Visualization of participants by their countries’ from the projects listed here.
With this project, I would try to represent participants and mentors participating in OLS on the map by their countries, and year of participation. I am planning to achieve this using Mapbox and OpenStreetMap. When hovering over a particular flag we can see that particular participants/mentors all info which is listed here or this one.
I would like to make something like this but would do a lot of brainstorming about design and representation. Also, we can add something like showing mentors vs ols-1/2/3/4 participants or showing number per country, or anything else creative. The next step would be to implement this on the official site of OLS. I want to practice my coding and visualization skills through this project and would appreciate the opportunity to meet, interact and work with like-minded people.
Mentored by: Patricia Herterich
Keywords: Open Science, Community Building, Open Education, Engagement
In this project we want to develop and implement new ways of building, engaging and maintaining the community around the TU Delft Open Science MOOC. We are part of the teaching team of the TU Delft Open Science MOOC called: ‘Open Science: sharing your research with the world’. The MOOC’’s next run starts in May 2022.
The course runs for 6 weeks and discusses a variety of open science topics, course materials are also available on TU OpenCourseWare.
The first Open Science MOOC started in 2018 and on average the course attracts about 1000 participants from an international environment. As the course runs participants engage with the teachers and each other through discussion forums. Here they introduce themselves, post assignments, and share and reply to each other’’s thoughts. While a few participants actively contribute and respond in the fora, engagement is still quite limited. Moreover, there is not yet a strategy in place to maintain the community after the course has finished. We would like to strengthen the community building taking place during and after this course by implementing additional strategies to engage participants during the course run and keeping up with participants after the course has finished.
Mentored by: Renato Alves
Keywords: Open Source, Reproducibility, Community, Open Infrastructure, Research
Binderhub is a service that allows users to share reproducible interactive computing environments through public code repositories. The subject of our project, Hub23, is an organisational deployment of Binderhub, designed to allow Turing Researchers to use binder (the user interface) to collaborate on repositories internal to Turing. This is sometimes necessary if the underlying repository can not be shared for some reason, or is not yet ready to publish openly. During the OLS program, we aim to build an open community around Hub23 to help to guide future technical developments, and encourage use and contributions from the wider Turing community. We will host a series of Zero-to-Binder workshops aimed at introducing Turing researchers to regular binder, followed by structured discussion of what the ideal features of a collaborative reproducible environment for research would be. Any conclusions and subsequent technical development will be fed upstream to Binderhub, and we also aim to open source the methodologies used to create an internal binderhub deployment, allowing other organisations to do so.
Mentored by: Sara El-Gebali
Keywords: neuropsychology, neuroimaging, data sharing, cognitive neuroscience, clinical neuroscience, data visualization, meta-analysis
We aim to build an online platform and community that allows open sharing, storage, and synthesis of clinical (meta)data, crucial for the development of modern, transdiagnostic, FAIR neuropsychology. First, published peer-reviewed papers will be scrapped to collect already available (meta)data. Second, our platform will allow direct uploading of clinical brain maps and their corresponding metadata.
A basic automated preprocessing and data-quality check pipeline will be implemented. Key data will be automatically extracted, synthesized, and made available alongside the one directly uploaded. All the available demographic, behavioral, clinical, and cognitive data will be properly organized and mapped onto the neural data to allow statistical analysis (i.e., data-driven lesion-symptom mapping). Ultimately, probabilistic maps synthesizing transdiagnostic information on lesion-symptom mapping would be constantly updated as more data are gathered. To this end, data visualization will be critical (e.g. https://speechbrainviewer.com/). Overall, the platform will
Mentored by: Sara Villa
Keywords: open education, student training, community building, educational resources, neuroscience
Open science is vital for reproducible, fair, and rigorous research. For its principles to thrive, we need OS practices to be shared and adopted by as many scientists as possible, from the earliest stages of their career. A 2017 survey by the European Commission reports that, among 1277 researchers at all career stages, the majority were unaware of the OS concept, and had never attended an OS initiative (from the Open Science Skills Working Group Report, July 2017).
For open research to become an established reality, those who are moving their first steps into research must have the opportunity to develop the necessary skillset to apply and disseminate the OS framework. “Open Science, Open Future” aims to be an educational resource to be used online by young scientists: undergraduates, MSc students, and potentially high-school pupils. The curriculum will consist of several modules explaining why each aspect of the OS practice can improve research and make it fairer (e.g. best practices in sharing protocols, storing data, publishing, collaborating). I’m the co-founder of a pan-european collective of scientists, https://biotop.co/, aiming at rethinking the way we do science. Fellow members are willing to take part to the project.
Mentored by: Sebastián Ayala Ruano
Keywords: AI, Cancer, Diagnostics, Digital pathology
Open Science for Improve diagnostics of Cancer through Artificial Intelligence and Digital Pathology.
Cancer is becoming increasingly prevalent among the group of treatable diseases in African countries. In sub-Saharan Africa, only 10% of histopathology needs are met and this is a major barrier to comprehensive management of cancers
Diagnosis of cancer relies on histology in nearly 80% of cases, cytology in 10%, and clinical diagnosis in 10% (1). There is, therefore, an urgent need to develop a rapid, highly sensitive and diagnostic tool for the diagnosis of cancers, to increase cancer treatment efficacy and reduce overtreatment of tumors clinically suspicious for malignancy. We propose a hybrid diagnosis method with a deep Learning algorithm applied on hematoxylin and eosin histology slides. Digital microscopy and telepathology were already successfully used to mitigate the lack of pathologists in Cameroon, thus confirming the availability of a robust dataset for our project (1). Following splitting into training, validation and test sets, we will use CNNs as algorithms on the collected images to train the algorithm before deployment and tests. In addition to automated diagnostic, the developed program will have specific features such as sample information storage and tracking software as well as image optimization and analysis tools.
By: Achintya Rao
Mentored by: Yo Yehudi
Keywords: community management, open and reprodicible data science, Artificial Intelligence, community white papers
The “AI for Science and Government” (ASG) programme at The Alan Turing Institute seeks to produce three community-led white papers that will capture the outcomes of research into deploying AI and data science in priority areas to support the UK’s economy. The papers will also highlight advances in practices towards open and reproducible research in the fields of AI and data science. The process of authoring the white papers will itself be collaborative, open and transparent, soliciting contributions from the wider ASG community at every step of the way.
Mentored by: Mayya Sundukova
ARPHAI is an interdisciplinary research consortium, whose mission is to develop technological tools and recommendations to anticipate and manage epidemiological events. ARPHAI pilots data-driven open source tools using artificial intelligence and data science towards upgrading Argentina’s electronic health record (EHR) system. ARPHAI is part of the Global South AI4COVID Program.
ARPHAI includes persons from 20 institutions. ARPHAI started in October 2020 and has grown very fast from scratch. More specifically, ARPHAI is piloting three EHR-based components in parallel to anticipate and detect potential epidemic outbreaks
There are two additional lines of work ARPHAI undertakes that are transversal to these three research developments, which include a) diversity, equity, and inclusion (DEI) with a focus on gender and b) responsible use of health data.
Keywords: Bioinformatics, data, astrobiology, biosignatures, life evolution, game theory
The project focuses on building tools to understand the evolution of life. We develop bioinformatic tools to determine evolutionary processes to detect early stage life development. The project looks at data from two specific parts of detecting life - co-evolution of life and environment and biosignature assessment within the context of habitability. We use data from current experimental projects and develop new models to aid the growth of astrobiology search for life. The platform will cater to multiple sections such as- data management from all astrobiology projects, experiments, research labs and conferences; new tools to analyse data, predictive model section to simulations from the data set and collaborative forum to encourage citizen science.The platform will help create open source bioinformatic tools to help detect biosignature, assess habitability, promote involvement within astrobiology. In addition to using bioinformatic tools, a part of the platform will use game theory and gamification to test the citizen science component. Using both the platform as a destination for tool testing and science education, we hope to advance the research in astrobiology.
By: Juyeon Kim
Keywords: Collaboration, building trust, intersectoral collaboration, Emotional/Physical/Nutritional diet for brain, global connectivity, Digitalization, Incentives to public and scientists
I am a civil engineer with a drive to impact the knowledge sharing through open science.
Abraham is an ecological researcher based at the University of the Witwatersrand, Johannesburg, South Africa. He is interested in how climate, fire, and large mammal herbivores shape grassland and savanna ecosystems in space and time. This knowledge is valuable for assessing current ecological theory, guiding successful ecosystem conservation and restoration, and understanding roles of humans in ecosystems.
Innovative, problems solver, community builder and team player, I hold two masters degrees in computer sciences and information systems. I am interested in contributing to solve community issues using ICT including cutting edge technologies such as ML, AI, and IoT.
I am a first-year PhD student at the Inorganic Systems Engineering group of TU Delft. In collaboration with an industry partner, I do research in data-driven catalyst discovery.
I am an incoming assistant professor at The University of Amsterdam, working in the field of astrochemistry/astrobiology. I love to teach and my work motto is doing fun stuff with nice people. I talk a lot and cannot properly function without coffee :)
I’m the Community Manager for The Turing Way @ The Alan Turing Institute, and an anthopologist by training. I was previously a Frictionless Data Reproducible Research Fellow at the Open Knowledge Foundation, and am currently a Fellow at the Internet Society. I also co-curate The Re:Source Project, which aims to support labor movements in supply chains through open data. In my past and present roles, I aim to contribute to the open ecosystem, and the research and tools that enable it.
I’m a junior student pursuing a Bachelors’s in Computer science studies. I am a Data Science and machine learning enthusiast. I like to travel , read, dance and listen to taylor’s music:)
I am a Training Officer at the Alan Turing Institute and a digital history researcher at the New College of the Humanities. I’m interested in historical mythmaking and misinformation.
Hi - I’m Ayesha and I’m interested in pedagogy and education; community building and forming meaningful connections; and personal development and growth. I also love cycling - (on-the-road, semi-competitive, all-the-gear-no-idea kind of cycling), good food and a gripping crime drama series!
For fun: I am very into catch and release fly-fishing and fly tying as well as other outdoor activities. I also do a number of crafts at varying degrees of success! Academically: I am nearing submission of my joint Ph.D. between North West University and Oslo University. I research sanitary and phytosanitary measures (SPS) in the context of barriers to trade in the South African red-meat industry with particular focus on the past and ongoing challenges that have arisen with the outbreak of foot-and-mouth disease in the country. I have followed a mixed methodology approach which includes qualitative research by means of semi structured interviews and quantitative research by means of a content analysis entirely applied through R programming. I am Zimbabwean born, but call Johannesburg (South Africa) home at the moment.
Umar Ahmad is currently the Head, Department of Anatomy at Bauchi State University, Nigeria. He is also a founder and CEO of BioSeq, a bioinformatics company that translates omics data into informative knowledge by providing quality high-throughput sequencing (NGS) data analysis. His work in basic and translational research is focused on developing targeted therapy for human bladder cancer, colon and lung cancers with primary focus on genomics (WGS, WES) and transcriptomics (RNA-Seq, scRNA-Seq, Microarray) data integration to investigate the regulatory pathways that drive tumour recurrence and progression. Additionally, Umar works in an international team of scholarly professionals at AfricArXiv - the pan-African Open Access portal – towards increased discoverability of African research output. His role involves facilitating manuscript submission moderation and quality assurance as well as representing AfricArXiv at international meetings, events and webinars. At the Science Communication Hub Nigeria, he supports a team that provides mentorship, implements training and community building for the next generation of Nigerian scientists. Umar is a fellow of Accelerating Science and Publication in Biology (ASAPbio), a mentee and a member in The Carpentries community and a member of Open Bioinformatics Foundation. He is also the current Regional Coordinator (North East) of the Nigerian Bioinformatics and Genomics Network (NBGN). Moreover, Umar maintains a community of scientists who are passionate about bioinformatics in a slack workspace called Bioinformatics Hub to facilitate sharing of bioinformatics knowledge in Nigeria. (Link: https://docs.google.com/document/d/14ayo1wHRpDvF-L5yHaBHyEqXW29EqEApfCtf3F3xiq4/edit?usp=sharing)
I am a Research Data Scientist at the Alan Turing Institute. An experimental psychologist by training, I moved to the research engineering group to be part of research projects that are more focussed on being open and reproducible!
I am a cheerful person, and the last year I have to learned to have more patience to deal with various situations in my life I have been able to count on the support of my friends
I am an early career researcher with a deep interest in past plant technology and responsible research. My research aims at identifying plant fibre remains preserved in archaeological contexts and in museum collections. For this, I combine micro (comparative anatomy, phytoliths) and macro studies (plant morphology and indigenous/local knowledge) with data gathered from experimental archaeology
Archaeobotanist and ethnoarchaeologist interested in dryland agriculture
I am a Mathematician and hold a Ph.D. in Cybernetics, currently working as a NeuroAI researcher to develop brain-augmented AI systems. I have been involved with several open sources (e.g. Linux software development community of Turkey) and open science (Brainhack, OHBM, OLS) communities and worked on various projects for the dissemination, training, and management of open science/source projects and communities. I developed guidelines and educational materials and organized many events and training courses to train government and military officials, students, and scientific researchers. I love creating means to bring community members with diverse backgrounds and expertise.
Medical student Associate editor of the Journal of the scientific society of medical students of the Universidad Mayor de San Simón “Revista Científica Ciencia Médica” Junior Researcher Auxiliary of the journal of the faculty of medicine of the Universidad Mayor de San Simón
I am a senior Bioengineering student at UTEC in Peru. I have been part of research projects involving synthetic biology and biomaterials. With knowledge of bioinformatics and analysis programs. I enjoy sharing science and technology to students through my participation in open programs like volunteers and organizations that promotes research and curiosity.
Highly motivated, inspired, and passionate to the open science and open scholarship movement. It is one of my greatest values and interests engaging people on discussing topics, curating, and organising discussions and events. I am deeply curious and invested in continuous learning and self-growth.
I’m an Open Archaeobotanist specialising in phytolith research. I’m currently working on building a community of open scientists in my field to address issues such as data sharing, FAIR data, open access and upskilling researchers in open science skills. I’m also working as a Senior Community Manager at the Alan Turing Institute on the project across the Health Programme and I am core team member of The Turing Way.
Emmanuel Adamolekun is a Research fellow with Helix Biogen Institute, Ogbomosho, Nigeria ,a research organization focused on accelerating research in life through in-depth technical skills, training and capacity building in Bioinformatics and Genomics. Emmanuel graduated with a Bachelor’s degree in Medical Laboratory Science from the prestigious Ladoke Akintola University of Technology, Ogbomosho, Oyo State, Nigeria. He is currently a member of the Education and Internship committee of the International Society for Computational Biology-Student Council (ISCB-SB). He is a member of the International Society of Computational biology (ISCB) and African Society Bioinformatics and Computational Biology (ASBCB).
I’m a biotechnologist and SynBio Africa emerging leader in synthetic biology and biosecurity fellow working with Beneficial bio to locally produce reagents and equipment for molecular biology research and application. My passion for Open Science and research led me to meet and join amazing people and communities in their efforts to impact the global open science landscape including Open Bioeconomy Lab, AfricaOSH, Africa Makers Gathering, and Open Science Shop. I see a lot of potential in distributed manufacturing and over the past years, I’ve been working to democratize global access to affordable and impactful scientific instruments. Fervant advocate of Open Science in Africa I’ve been shar
I’m a university technician in International Relations from the National University of Lanús (UNLa)- currently - am studying for a bachelor’s degree in Integration Processes and International Economic Relations at the same university. I have experience as a consultant in research projects financed by international organizations such as the Inter-American Development Bank and the World Bank (IADB-IBRD). He currently works as a Semi-Senior research assistant at CIECTI-UIME and an operational assistant for the coordination of technological tools for the ARPHAI project.
Frédérique is the publishing officer of TU Delft OPEN Publishing, the open access academic publisher of TU Delft. Her role consists of helping researchers to disseminate their research openly though various streams such as Open Access Books, Open Access textbooks and Open access journals. She is an advocate of open science, open peer-review and fair rewards &recognition.
I currently work at National University of Jujuy and the National Scientific and Technical Research Council - Argentina. Most of my work has focused on the archaeobotanical study of ancient starch and phytoliths from dental calculus, ceramic residues and sediments in pre-Hispanic sites in Argentina.
I’m a Research Software Engineer based in Bristol working on a cloud platform for data sharing and analysis.
My background is in molecular biology, I only transitioned to coding and research software at later stages in my career. I’m the co-founder and CEO of Ersilia, a small nonprofit working to support researchers in low resource settings apply ML to their research in infectious diseases. I’m an enthusiast of Open Source, creating communities and making sure people can actually use the cool tools being developed around the world!
Currently studying towards a MSc in philosophy of the social sciences at the LSE. Curious about the values that drive human action, and the nature of collaboration.
Jafsia is a data scientist working on health and particulary neglected diseases
Senior student of Genetics & Biotechnology at UNMSM, Peru. Member of MikuyTec synbio research group, member of Computational Biophysics Lab at UNIFAL-MG, Brasil and president of SciHack, a DIY Bio community lab aiming to democratize biotechnology.
I am an archaeobotanist interested in how late prehistoric societies interacted with their environment in terms of plant food acquisition and transformation practices, particularly during the Neolithic and Bronze Age.
Proactive, Courageous, Positive
I am trained formally in Statistics. I have worked as a Software Quality Engineer - Statistician.
PhD in Biomedical Science, with a deep appreciation for living systems at all scales, and an optimism about the lessons that humanity can take from Nature.
Enthusiastic advocate for the fundamental computational skills and practices required for reproducible research.
I am a tenured researcher leading a collaborative health data science research group. I also work to improve data analysis teaching and practice. I co-founded MetaDocencia, an open, collaborative, and Spanish-speaking education community. One of the roles I enjoy most is mentoring and teaching others.
I have a background in both Pharmacy and History, and I combined these fields during my PhD, where I text-mined digitized newspapers to analyze historical debates on morphine. I have always had a passion for education, which is why I am so happy to be working as an open science and academic skills teacher at TU Delft library since 2021. I am excited to join this community and learn more about open science!
My background is in Zoology and I have a PhD in bird flight aerodynamics, mostly working with hawks and eagles! I recently joined the Alan Turing Institute as a research data scientist, working on lots of projects. I have great interest in education and awareness of reproducibility in science and research, especially for life scientists. I’m a self taught programmer and have been involved with Software Carpentries and The Turing Way.
Role in OLS:
Director of Partnerships and Strategy
Malvika Sharan is a Senior Researcher at The Alan Turing Institute, where she leads a team of community managers and co-leads The Turing Way, a community-led handbook on data science. She is a co-founder of Open Life Science, and an active contributor of several open source/science projects. Connect with her on topics such as community building, open science, strategic collaboration and representation of marginalised members in leadership.
Maria Andrea Gonzales is a 4th year Bioengineering undergraduate in UTEC (Lima, Peru). She is currently working in a variety of biotechnology research projects as well as science communication projects. Maria Andrea is passionate about the application of synthetic biology and protein engineering for the development of open-source therapeutics as well as a sustainable food industry.
I am a neuroscientist passionate about education and science communication. Through the OLS initiative, I’d like to convince as many young researchers as possible that open science is better science!
Research student developing point of care diagnostic tool for malaria, He’s enthusiast of open science tools with skills in R programing and other open access software for bioinformatic analysis
A biohacker in progress
Background working in NGOs across campaigns, training and skills policy, currently situated in the Turing Institute. I’m passionate about transparency, equity and aim to carry this across my professional and personal life. I love sea swimming and very loud music!
Valentia, Honradez y Respeto
I am trying to be a good molecular biologist. I think that learning new things and sharing them in this field is great.
A Machine Learning enthusiast willing to learn, share and giving back to the community with soft & tech skills.
A research translator and innovation architect in the life science industry
22 years old and Bachelor in Bioengineering. I like strawberries, plants, arthropods, space and genetic modifications. Future Biohacker but not like the ones on Netflix.
I’m a Brazilian cognitive neuroscientist studying the neural architecture and dynamics of human intelligence, with a focus on elementary mathematics. I live in San Francisco and I love music, art, photography, cooking, nature and endurance sports.
I am the community manager for the “AI for Science and Government” research programme at The Alan Turing Institute, with a background as a science writer communicating high-energy particle physics.
I’m a physiotherapist working in the private sector in South Africa.
I have a background in educational resource design and development, and a keen interest in exploring how to make online learning experiences as engaging as possible.
Currently, I am a Research Assistant for the “Co-Creating Culturally Appropriate Research Ethics” (CARE) project at Nazarbayev University. I am also a Frictionless Data for Reproducible Research Fellow and interdisciplinary human rights researcher. For the last nine years of my research, I have studied such topics as gender, sexuality, nationalism/racism, disability, mental health issues, and epistemic (in)justice - mainly through the lenses of post/decolonial, critical pedagogical, feminist, and indigenous theories.
I received my PhD in Neurolinguistics from Northwestern University under the supervision of Dr. Cynthia K. Thompson and completed postdoctoral training in cognitive neuroscience under the supervision of Dr. Maria Luisa Gorno-Tempini at the University of California San Francisco (UCSF) - Memory and Aging Center. My neurobiology of language and behavior (NoLaB) lab focuses on the two lines of research: the neurocognitive correlates of the lexical system and its relation with emotions and other cognitive systems.
I have a Ph.D. in Biology (neuroscience) where I acquired diverse tools for data analysis. In the last years, I became interested in the impact of new technologies and their ethical implications in Public Health
Rika, a 4th year undergraduate student in Bengaluru India majoring in Electronics and Communication. She is currently pursuing her project work at RRSC ISRO and is passionate about women in stem and space. She started WOAA India in 2020.
Valentina Borghesani, Ph.D., is an Italian cognitive neuroscientist currently working as senior postdoctoral researcher within the CNeuroMod project at the Psychology Department of the Université de Montreal. Her research focuses on the neuro-cognitive correlates of semantic knowledge which she investigates with both neuroimaging techniques (fMRI, MEG) and neuropsychological data. She deeply cares (and is very active in) bridging neuroscience & ethics, community, diversity, environment, and the arts. After a PhD in France and postdocs in California and Quebec, Valentina is starting as an Assistant Professor at the University of Geneva in September 2022.
I am a Doctor in Social Sciences, University of Buenos Aires (UBA), Master in Political Science and Sociology, Latin American Faculty of Social Sciences (FLACSO), and Anthropologist (UBA). I have extensive experience in interdisciplinary research and intervention projects on free technologies, co-production of knowledge, and data. I’m currently working as a researcher at the Interdisciplinary Center for Studies in Science, Technology, and Innovation (CIECTI) in the area of Digital Economy and the ARPHAI project. Also, I am an activist for Free Software and Knowledge, and I enjoy working in heterogeneous and interdisciplinary teams where we all learn from each other. To have into account: I reach top productivity in Spanish. I find it more difficult to work in English as it is not my native tongue.
Vicky Hellon is currently a community manager based at the Turing Institute, working on the Turing-Roche partnership. She has a BSc in Biomedical Science from the University of Sheffield and previously worked for Health Data Research UK and in Open Access Publishing roles at Springer Nature and F1000Research.
I’m a very curious person who enjoy teaching and learning. My personal interests are very varied, from science, education and health to plant-based cooking, gardening and composting. Since my PhD project I have worked on different data projects and on the way I discovered I’m particularly interested in data visualization. I feel particularly motivated by projects with socio-environmental impact.