Open Source

EMBL-EBI seeks a Bioinformatics Developer for DECIPHER, a platform supporting rare-disease research and clinical interpretation of genetic variation. The developer will evaluate and integrate genomic and phenotype resources, deploy analysis tools, design database structures and interfaces, investigate data problems and work with clinical and research collaborators. The role is based in Hinxton with hybrid working and may be full time or 80% time. The advert gives a closing date of 8 October 2026 at 23:59 CET.

Innovate UK funds preparatory work to establish the Medicines Manufacturing Data Institute, a secure national hub for sharing and using medicines-development and manufacturing data. Phase 1 supports consortium formation and preparation of a phase 2 proposal. The competition has a total funding pool of GBP 500,000; this is not a per-project award claim. UK registered businesses, academic institutions, research and technology organisations, charities, nonprofits and public-sector organisations may lead or apply alone. Applications opened on 7 September and close on 14 October 2026 at 11:00 UK time.

The National Library of Medicine supports computational methods that make biomedical research assets easier to curate and reuse at scale. Projects can address data, software and models through scalable, reliable approaches, including machine learning. Clinical trials are excluded. The award supports up to USD 250,000 in direct costs per year for up to four years. The next deadline available to new applications is 15 January 2027; the October 2026 date is for resubmissions and related application types.

When meta-research (research on research) makes an observation or points out a problem (such as a flaw in methodology), the project should be repeated later to determine whether the problem remains. For this we need meta-research that is reproducible and updatable, or living meta-research. In this talk, we introduce the concept of living meta-research, examine prequels to this idea, and point towards standards and technologies that could assist researchers in doing living meta-research. We introduce technologies like natural language processing, which can help with automation of meta-research, which in turn will make the research easier to reproduce/update. Further, we showcase our open-source litmining ecosystem, which includes pubget (for downloading full-text journal articles), labelbuddy (for manually extracting information), and pubextract (for automatically extracting information). With these tools, you can simplify the tedious data collection and information extraction steps in meta-research, and then focus on analyzing the text. We will then describe some living meta-research projects to illustrate the use of these tools. For example, we’ll show how we used GPT along with our tools to extract information about study participants. Essentially, this talk will introduce you to the concept of meta-research, some tools for doing meta-research, and some examples. Particularly, we want you to take away the fact that there are many interesting open questions in meta-research, and you can easily learn the tools to answer them. Check out our tools at https://litmining.github.io/

Cells and microorganisms are motile, yet the stationary nature of conventional microscopes impedes comprehensive, long-term behavioral and biomechanical analysis. The limitations are twofold: a narrow focus permits high-resolution imaging but sacrifices the broader context of organism behavior, while a wider focus compromises microscopic detail. This trade-off is especially problematic when investigating rapidly motile ciliates, which often have to be confined to small volumes between coverslips affecting their natural behavior. To address this challenge, we introduce Trackoscope, an 2-axis autonomous tracking microscope designed to follow swimming organisms ranging from 10μm to 2mm across a 325 square centimeter area for extended durations—ranging from hours to days—at high resolution. Utilizing Trackoscope, we captured a diverse array of behaviors, from the air-water swimming locomotion of Amoeba to bacterial hunting dynamics in Actinosphaerium, walking gait in Tardigrada, and binary fission in motile Blepharisma. Trackoscope is a cost-effective solution well-suited for diverse settings, from high school labs to resource-constrained research environments. Its capability to capture diverse behaviors in larger, more realistic ecosystems extends our understanding of the physics of living systems. The low-cost, open architecture democratizes scientific discovery, offering a dynamic window into the lives of previously inaccessible small aquatic organisms.

This webinar will focus on spike sorting analysis with SpikeInterface, an open-source framework for the analysis of extracellular electrophysiology data. After a brief introduction of the project (~30 mins) highlighting the basics of the SpikeInterface software and advanced features (e.g., data compression, quality metrics, drift correction, cloud visualization), we will have an extensive hands-on tutorial (~90 mins) showing how to use SpikeInterface in a real-world scenario. After attending the webinar, you will: (1) have a global overview of the different steps involved in a processing pipeline; (2) know how to write a complete analysis pipeline with SpikeInterface.