Lab Informatics: LIMS, ELN & Research Data Systems
Laboratory Information Management Systems (LIMS) track samples, workflows, and results across a lab's operations; Electronic Lab Notebooks (ELNs) replace paper notebooks with searchable, timestamped, shareable digital records; and platforms like OSF (Open Science Framework) and protocols.io add project-level and protocol-sharing infrastructure on top. This sub-cluster covers how these systems differ, how to select one for a given lab's scale and regulatory context, and how they connect to instrument data and downstream analysis — a genuinely high-value, underserved topic (LIMS alone measures ~40,500 monthly US searches at a $20+ CPC, informational intent, with almost no existing CASRAI coverage).
Guides
REDCap User Rights and Data Access Groups (DAGs)
What REDCap User Rights (form-level, field-level, export, create/delete) control, what a Data Access Group restricts, and the setup mistakes that leak cross-site data.
How to Request an NSF ACCESS Compute Allocation
A step-by-step walkthrough of requesting an NSF ACCESS supercomputing allocation: choosing Explore, Discover, Accelerate, or Maximize, what the request must justify, submission mechanics, review timelines, and renewal.
How to Get an Interactive Session on an HPC Compute Node
How to use salloc and srun –pty to get an interactive shell on an HPC compute node instead of running work on the shared login node, and why login-node usage policy exists.
sacct and seff: Checking Slurm Job Resource Usage
How to use sacct and seff to check what a Slurm job actually used — state, elapsed time, memory, CPU efficiency — and right-size future resource requests.
Requesting a GPU in a Slurm Batch Job
How to request GPUs in a Slurm batch job with –gres=gpu:N, –gpus=N, and the newer –gpus-per-task/–gpus-per-node forms, target a specific GPU type, avoid the two mistakes that waste GPU-hours, and verify the GPU is visible with nvidia-smi.
Slurm Priority and Fairshare: Why Your Job Is Waiting in the Queue
Why a submitted Slurm job doesn’t start immediately: how the multifactor priority plugin scores fairshare, job age, job size, partition and QOS, and how to read squeue and sprio to see exactly where a pending job stands.
Slurm –nodelist, –exclude, and –constraint: Targeting or Avoiding Compute Nodes
A practical guide to Slurm node-selection flags: –nodelist to require named nodes, –exclude to avoid them, and –constraint to request nodes by feature instead of by name.
Cancelling Slurm Jobs with scancel
How to cancel Slurm jobs with scancel: by job ID, by job array (whole array vs. one task index), and by username, plus what differs between cancelling a pending job and a running one, and how to handle a runaway array or a job stuck on a bad dependency.
How to Write an Sbatch Job Script
A practical guide to writing correct Slurm sbatch job scripts: the shebang, the #SBATCH directive block, which directives matter most, a complete worked example, and the difference between requesting resources and your program actually using them.
Sharing a Reproducible Conda Environment
A plain conda env export rarely rebuilds cleanly on someone else’s machine. This guide covers why (platform-specific builds, unpinned transitive dependencies, channel priority) and what actually works: –from-history plus deliberate pinning, and conda-lock for real multi-platform lock files.
Conda, Pip, and Mamba in One Environment: Order Matters
Mixing pip installs into a conda or mamba environment is normal, but conda’s solver can’t see what pip did. Here is the safe order of operations and how to declare both in one environment.yml.
Embarrassingly Parallel Jobs: How to Recognize and Run Them
What makes a workload embarrassingly parallel, how to run one on an HPC cluster with Slurm job arrays or GNU parallel, and the hidden dependencies (shared files, aggregation steps, rate-limited APIs) that mean it isn’t.
Slurm Job Arrays: Running Hundreds of Similar Jobs Without a Submit Loop
A practical guide to Slurm job arrays: –array syntax, using SLURM_ARRAY_TASK_ID to index per-task input, why arrays beat a submit loop, and array-specific throttling and cancellation.
Open-Source LIMS: SENAITE, OpenELIS, and What Free Actually Costs
A concrete look at SENAITE and OpenELIS Global — the two genuinely live open-source LIMS options — and the hosting, integration, GxP validation, and support costs that “free” software does not eliminate.
LIMS Pricing: How Laboratory Information Management Systems Are Costed
How LIMS (Laboratory Information Management System) pricing actually works: subscription vs. license models, per-user vs. per-sample billing, and the implementation and validation costs vendors rarely quote up front.
What Is a LIMS? Laboratory Information Management System Explained
A Laboratory Information Management System (LIMS) tracks lab samples, workflows, and results with a full audit trail. This guide explains what a LIMS does, how it differs from an ELN and a LIS, and the selection criteria that matter in practice.
