Processes

The fundamental unit of lab work — every activity that transforms inputs to outputs.

What is a process?

A process represents a specific activity in your research workflow. It records what was done, who did it, what protocol was followed, what inputs were used, and what outputs were produced. Processes are the backbone of provenance tracking in Libre Biotech.

Process categories

Category	Description	Typical inputs	Typical outputs
Extraction	Isolating material from a source	Tissue, organisms	DNA, RNA, protein
Sample Preparation	Preparing samples for downstream use	Extracted material	Libraries, pooled samples
Sequencing	Generating sequence data	Libraries	FASTQ files, run metrics
Measurement	Quantitative assessment	Any sample	QC metrics, concentrations
Data Transformation	Computational analysis	Data files	Alignments, assemblies, annotations

Creating a process

Click New Process on the dashboard, or navigate to Research → Lab Notebook. The creation wizard guides you through four steps:

Step 1: Basics

• Title — A descriptive name (e.g., "DNA extraction — soil samples batch 1")
• Summary — Brief description of the experimental procedure
• Process Category — Determines what configuration options appear in Step 2 (see categories table above)
• Status — Draft, In Progress, Completed, or Needs Review
• Project — Which project this process belongs to (required for access control)
• Protocol — The procedure that was followed (selected from the protocol library)
• Process Date — When the work was performed

Step 2: Configuration

The options shown depend on the category selected in Step 1:

Category	Configuration options
Sample Preparation	Create output samples — set label, description, material type, and optionally link source samples from earlier processes
Measurement/Assay	Set assay type from the OBI ontology
Sequencing Submission	Select sequencing platform (Illumina, Nanopore, PacBio) and choose samples to submit
Data Transformation	Record tool name/version, command line, input samples, and optionally link to an existing analysis run (see below)
Management / Other	No additional configuration required

Step 3: Participants

You are automatically added as the Operator. Change your role if needed (Owner, Contributor, Reviewer, etc.). If other group members were involved, expand "Add another participant" to include them.

Step 4: Review & Create

Review all details before submitting. The review shows title, category, status, project, protocol, process date, category-specific details, and participants.

Recording data transformations

Data transformation processes record computational analyses — either external (R scripts, local pipelines, cloud HPC) or on-platform (CWL pipelines). There are two paths:

External analyses

When you select Data Transformation as the category, Step 2 of the wizard lets you record:

• Tool name & version — e.g. "DESeq2 v1.42.0" or "Salmon v1.10.1"
• Command / description — paste the command you ran or describe the workflow
• Input samples — select which samples were used as input to the analysis
• Link to existing analysis run — optionally link a completed on-platform run that wasn't auto-linked

The resulting process page shows an External Analysis card on the Pipeline/Script tab with the tool details and command you entered.

On-platform analyses

When a pipeline run completes (or fails) on the compute server, the system automatically creates a data transformation process linked to the run. You don't need to create these manually — see Analysis Pipelines for details.

After creating a sequencing submission

After creating a Sequencing Submission process, you can link it to actual sequencing run data:

1. Link Run — Click "Link Run" in the Quick Actions sidebar to search for a QC run from the sequencing dashboards (NanoporeQC, IlluminaQC, or PacBioQC). This connects the sequencer's quality metrics to your ISA process
2. Submitted Samples tab — Shows which samples were submitted for sequencing, with their status
3. QC Metrics tab — Once a run is linked, displays yield, quality scores, and other metrics from the sequencer

Recording measurements

After creating a Measurement/Assay process, you need to link samples and add measurement values:

1. Link samples — On the process page, click Link Samples in the Quick Actions sidebar. Select the samples you measured (only samples from the same project are shown)
2. Add measurements — On the Samples tab, click Add Measurements next to each sample. Enter values (e.g. concentration, RQN, fragment length) and select units from the Unit Ontology
3. View the matrix — The Measurements tab shows all values in a grid: samples as rows, measurement types as columns

Process page

The process view is organised into tabs:

Overview tab

• Process metadata (name, category, protocol, dates)
• People involved (researcher, technician) with roles
• Ontology annotations
• Status and notes

Samples tab

• Input samples — Materials consumed or used by this process
• Output samples — Materials produced by this process
• Add existing samples as inputs, or create new output samples

Files tab

• Upload files directly to the process
• Link external files from the file system
• View, download, or unlink files
• Adopt orphaned files (files not yet linked to any process)

QC tab (sequencing processes)

• Search and link QC runs from Illumina, Nanopore, or PacBio dashboards
• Map QC samples to ISA samples
• View linked QC metrics

Review tab

• Request peer review of the process
• View review status and comments
• Sign off on completed reviews

Process chains and provenance

When the output samples of one process are used as input samples for another, a process chain is formed. This chain provides a complete audit trail.

Process: "Dissection"
  → Output: tissue_01

Process: "RNA Extraction" (input: tissue_01)
  → Output: rna_01

Process: "Library Prep" (input: rna_01)
  → Output: lib_01

Process: "Nanopore Sequencing" (input: lib_01)
  → Output: fastq files

You can visualise the complete provenance chain from any sample's page (see Samples).

Adding people

Each process can record who was involved:

1. On the process page, click Add Person
2. Search for a platform user
3. Assign a role (e.g., "Researcher", "Technician")
4. Optionally mark them as the primary researcher

Linking protocols

Processes reference protocols from the Protocol Library. This ensures reproducibility — anyone viewing the process can see exactly what procedure was followed, including version history.

Editing processes

Process metadata (name, notes, dates) can be edited by group members with Manager or Leader roles. Sample linkages and files can be modified by any group member.

All changes are tracked in the process audit trail.