LatchBio

Kit providers are enabling exploration of the farthest boundaries of biological possibilities by transforming cutting-edge biological solutions into accessible kits. However, these kits can generate 100s of TBs of data that can take months and vast computational infrastructure to turn into insights. Listen to Colin Ng, VP of AtlasXomics Inc., describe how quickly their customers can explore insights from raw data on Latch. 

We have learned over the past decade that sequencing RNA and DNA is not enough to develop drugs or understand basic biology. There are many experimental techniques that help scientists understand the epigenome, but ATAC-seq is likely the most widespread. However, making sense of this data is difficult, and running bioinformatics workflows is only a small piece of the full analysis lifecycle. The goal of ATAC-seq is to locate peaks of chromatin accessibility across the genome and examine how they change with covariates. This requires software that allows scientists to perform genome-scale operations and render peaks across multiple samples with low latency. To accomplish this, we showcase a suite of tools scientists use to interrogate ATAC-seq data, and outline how they fit into a broader data infrastructure suitable for interdisciplinary collaboration and long term data re-use. We start with the end reports, and work backwards to the sequencer, in a full analysis lifecycle to answer concrete biological questions: - How do peaks of accessible DNA vary between different samples? - Are there enriched motifs or functional annotations associated with these regions? - Where are genomic regions of chromatin accessibility? https://lnkd.in/g6Az_DRU

Avoid copying and pasting between spreadsheets and manually plotting your results. Calculate ΔCq, ΔΔCq, and fold changes, with access to underlying Python, by clicking a button on Latch’s qPCR Template. Test it out yourself with this interactive demo: https://lnkd.in/geQbFZNx

Most of the biotech industry runs on qPCR. Its low cost, simplicity and maturity has established the technique as a staple in many molecular biology workflows. However, the analysis of the downstream data is anything but standard. Most scientists spend hours passing files between Excel and GraphPad Prism, where they analyze data with error-prone spreadsheet calculations and manually plot their results. There is a need for modern analysis tools to manage the full lifecycle of qPCR data, supporting the following core steps: - The central and structured capture of qPCR machine outputs and experimental metadata - An automated and reproducible method for computing Cqs + ∆∆Cqs, and producing plots, backed by Python - Links between raw machine outputs, tables of Cq calculations and final plots Here we present the full analysis lifecycle of qPCR on LatchBio to answer the following biological questions: - How do my raw Cqs vary between wells? - What are the ∆∆Cqs for each condition? - How does the fold change of my target gene change between conditions? Read a deep dive on the analysis lifecycle - https://lnkd.in/g5vWi9rj

We're back! Lux Capital is running a Bio x ML Hackathon with EvolutionaryScale and Enveda Biosciences Bio from Oct 10-20! By bringing together the world’s top minds, we’re driving forward the next frontier of science with AI-driven tools and scientific imagination. Build on top of the latest foundation models like ESM3 (98B parameters, GPU access) and proprietary datasets to predict protein activity, model across therapeutic modalities, and develop next-gen biology applications. Model APIs, datasets & compute powered by Amazon Web Services (AWS), OpenAI, NVIDIA, DigitalOcean, EvolutionaryScale, Modal, LatchBio, Together AI, Enveda Biosciences, and RunPod. Open globally. Get started here: hackathon.bio

Visualize key insights from top differentially expressed genes via MA plots, heatmaps, and volcano plots in Latch's DESeq2 report. Analysis on Latch Plots is easily customizable with accessible and modifiable underlying Python code. Try out the Latch Plots experience yourself using this interactive demo! https://lnkd.in/gCA3axGU

Latch provides a native Nextflow integration that enables developers to use the existing nf-core/rnaseq codebase with minimal modifications and customize an intuitive graphical interface for scientists. Scientists can use interactive downstream visualizations, such as volcano plots, MA plots, and heatmaps, to understand their data. Read more below:

Latch Registry provides error-validated metadata capture for wet lab scientists and bioinformaticians to create a single source of truth for their experiments and bioinformatics results. Read more below.

Bulk RNA-seq continues to be the workhorse assay for most of the biotech industry. However, the data infrastructure for the storage, analysis and reporting of results is often lacking for this experiment. Disproportionate attention is placed on the bioinformatics workflows that process sequencing reads into gene counts, at the expense of the upstream and downstream infrastructure necessary for collaboration, compliance and future analysis. This includes: - Central and structured capture of data and experimental metadata - Reports that are accessible and usable by scientists - Links between raw experimental data, bioinformatics workflows, processed counts and final reports Bulk RNA-seq analysis is as much a human engineering project as a software problem and demands infrastructure where each component is centralized and accessible to different wet and dry lab teams. Here we present the full analysis lifecycle of this experiment on LatchBio to answer the following biological questions: - What are the gene counts in my sample? - What are the differentially expressed genes between conditions? - What are the key functions, pathways or ontologies associated with key genes? Link to a long form description of the lifecycle - https://lnkd.in/dgmvw5bU

It was great to talk with Colin Ng, VP of AtlasXomics yesterday during our webinar! We’ve been fortunate to partner with AtlasXomics Inc. to create a toolset that makes their customers’ data analysis automated and accessible without sacrificing flexibility.  If you couldn’t make it to our live webinar yesterday, you can still watch the recording here: https://lnkd.in/gvdvc3nm