Here we have curated a list of resources related to biomedical data science that might be helpful in your career.
Is your favourite resource missing from our list? Let us know at integrate@imm.ox.ac.uk
Inspiration Board
Below you'll find a series of activities and schemes that our survey respondents said had helped them in their career to help you find what works for you! For more information on our survey, see here.
We have also published a PDF list of useful communities and resources, which can be found at the bottom of this page.
Communities:
| Community name ↕ | Target Audience ↕ | Description ↕ | Link |
|---|---|---|---|
| Society of Research Software Engineering | Research Software Engineers | A society for those working in roles relating to research software engineering. | Society of Research Software Engineering
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| Turing Way | All | A slack channel which accompanies the Turing Way handbook, which promotes reproducible, ethical and collaborative data science. It is an open space for asking questions, learning about other’s work, and finding out about related events and projects associated with the Turing Way. |
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| Bioconductor | All | A diverse, collaborative and welcoming community that aims to train all levels in computational research and develop, support and disseminate free open-source software for biological data analysis. Bioconductor runs a free and active community on Zulip. |
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| Cancer Research UK Data Science Community | All | A slack channel welcoming all those interested in data driven approaches to cancer research. |
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| BioFAIR | All | An emerging community to bring together those working to make biological data more Findable, Accessible, Interoperable and Reusable. |
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| AI in the Biosciences (AIBIO) | All | A community building project supporting AI in the biosciences. |
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| Health Data Research UK | All | The national institute for Health Data Science in the UK. Open resources and events for anyone working with health data in the UK. |
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| Computational Abilities Knowledge Exchange (CAKE) | Digital Research Technical Professionals | Facilitates knowledge exchange and collaboration across the digital research infrastructure (DRI) communities across the UK. Signposts to many other relevant events, opportunities and and groups relevant to this community. |
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| ELIXIR | All | ELIXIR coordinates and develops life science resources and training across Europe so that researchers can more easily find, analyse and share data, exchange expertise, and implement best practices. ELIXIR runs regular community calls with multiple interest groups around specific areas. To find out if your institution is a member, see: https://elixir-europe.org/about-us/who-we-are/nodes/uk |
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| DisCouRSE | Digital Research Technical Professionals | DisCouRSE are trying to build a network of people working in or alongside digital Research Technical Professional (dRTP) roles. Their project focuses on leadership, career pathways and collaboration to support the development of the diverse community that is essential to make the best use of the UK's digital research infrastructure. |
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| STEP-UP/SCALE-Up | Digital Research Technical Professionals | STEP-UP aims to build a regional, London-based, platform to support the development of communities, skills and career opportunities for digital Research Technical Professionals (dRTPs). This work is now being expanded upon at the national scale through the SCALE-UP Network |
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Resource hubs:
| Resource name ↕ | Target Audience ↕ | Description ↕ | Link |
|---|---|---|---|
| Health Data Research UK Futures platform | All | Futures, powered by HDR UK is the UK's national learning platform for health data science, offering free, flexible learning to help researchers, healthcare professionals and data scientists develop skills in areas such as AI, programming, statistics and research methods. Learners can also explore our new career pathways, which showcase different career options in health data science and recommend relevant training to support progression. Popular courses include Bringing Software as a Medical Device to Market, Data Visualisation in the Health and Care Sector and Distributed Computing for Health Data. In addition to self-paced learning, HDR UK also offers a range of live webinars, workshops and events, which can be viewed on the HDR UK Events page. |
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| Computational Abilities Knowledge Exchange (CAKE) | Digital Research Technical Professionals | Facilitates knowledge exchange and collaboration across the digital research infrastructure (DRI) communities across the UK. Signposts to funding opportunities, events, and other initiatives within the DRI space. |
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| ELIXIR | All | ELIXIR coordinates and develops life science resources across Europe so that researchers can more easily find, analyse and share data, exchange expertise, and implement best practices. As well as linking to many helpful resources, ELIXIR also runs a flexible bursary scheme to support activities by those in the community. Membership is free for those in member organisations. To find out if your institution is a member, see: https://elixir-europe.org/about-us/who-we-are/nodes/uk |
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| Software Sustainability Institute (SSI) | Research Software Engineers | The UK national institute for research software. The SSI hosts various resources for training around research software, and also provides funding opportunities such as the Software maintenance fund, and SSI fellowships. |
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| PEDRI (Public Engagement in Data Research Initiative) | All | Training and resources to help guide public engagement activities around the subject of data research | PEDRI
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| Valuing Voices | All | A comprehensive tool and resource hub to help you plan and deliver equitable collaborative research projects. |
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| Teams Build Dreams | All | Based at the University of Manchester, Teams Build Dreams have a collection of case studies around team-science and also provide training to teams embarking on collaborative research projects |
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| UK Reproducibility Network (UKRN) | All | Resources for those looking to conduct responsible and reproducible research |
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| BioFAIR | All | An emerging community developing shared approached to implementation of FAIR. BioFAIR centre their activity around a people commons, a method commons and a data commons, and are also actively developing a training hub to support anyone working in biological research to make their data more open and FAIR. |
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Career Development
| Resource name ↕ | Target Audience ↕ | Description ↕ | Link |
|---|---|---|---|
| DIRECT Framework | All | The Digital Research Competencies (DIRECT) Framework was designed to help you to identify skills, define development pathways and progress your career in research software. |
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| EMBL-EBI Core Competencies | All | A competency framework encompassing multiple data-based roles to help you understand the skills and training you might find helpful to progress in your chosen career path. |
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| Liston Lab Careers resources | All | Resources from the lab of Adrian Liston at the University of Cambridge covering a variety of topics from building a diverse and productive lab team, to juggling motherhood and science. |
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Domain-specific Resources
| Resource name ↕ | Subject ↕ | Description ↕ | Link |
|---|---|---|---|
| Single-cell best practices | Single-cell analysis | (mostly python; Fabian Theis et al) Best practices of single-cell sequencing analysis. This book will teach you the most common analysis steps ranging from pre-processing to visualization to statistical evaluation and beyond |
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| Orchestrating Single-Cell Analysis book | Single-cell analysis | Orchestrating Single-Cell Analysis book aka OSCA (Lun et al) teaches users some common workflows for the analysis of single-cell RNA-seq data (scRNA-seq). This book will show you how to make use of cutting-edge Bioconductor tools to process, analyze, visualize, and explore scRNA-seq data. | Orchestrating Single-Cell Analysis book aka OSCA
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| Single cell RNA-seq data analysis with R (2019) | Single-cell analysis | Single cell RNA-seq data analysis with R (2019) (tutorial; several videos) This lecture series was recorded during the ELIXIR EXCELERATE course "Single cell RNA-seq data analysis with R" (27.-29.5.2019) | Single cell RNA-seq data analysis with R
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| 3blue1brown | Statistics | Mathematics with a distinct visual perspective. Linear algebra, calculus, neural networks, topology, and more. |
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| Explained Visually | Statistics | Explained Visually (EV) is an experiment in making hard ideas intuitive inspired the work of Bret Victor's Explorable Explanations. PCA, regression, probability, etc. |
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| The Markov-chain Monte Carlo Interactive Gallery | Statistics | Interactive Markov-chain Monte Carlo Javascript demos | The Markov-chain Monte Carlo Interactive Gallery
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| Modern Statistics for Modern Biology | Statistics | Book by Susan Holmes and Wolfgang Huber. A far-reaching course in practical advanced statistics for biologists using R/Bioconductor, data exploration, and simulation. | Modern Statistics for Modern Biology Book |