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Project Management

Effective data organization is crucial for managing antibody campaigns. AbLead uses Projects to group related sequences and structures.

Creating a Project

  1. Navigate to the Dashboard.
  2. Click File > Import Project.
  3. Enter a descriptive Project Name.
  4. (Optional) Add Notes (a description of the project, etc.).

Importing Sequences

To analyze antibodies, you must import sequence data and optionally associate it with structural models (PDB or mmCIF files).

Sequence Format Requirements

Your sequence file must contain amino acid sequences for antibodies, TCRs, or single-domain constructs. Minimally the variable domain (Fv), but full-length sequences are recommended. The system automatically detects and supports multiple formats (including FASTA, CSV, FASTQ, GenBank, EMBL, SwissProt, and Clustal).

  • Split Chains: Identify paired chains separately with matching base names.

  • Matching Names (FASTA, FASTQ, etc.): Use the same base name for paired chains, appending the appropriate chain suffix to allow the system to automatically pair them:

    • Antibodies (Fv): Append _LC (or _VL) for Light Chains and _HC (or _VH) for Heavy Chains.

    • TCR (\(\alpha/\beta\)): Append _TRA (or _VA, _alpha, _A) for Alpha Chains and _TRB (or _VB, _beta, _B) for Beta Chains.

    • TCR (\(\gamma/\delta\)): Append _TRG (or _VG, _gamma, _G) for Gamma Chains and _TRD (or _VD, _delta, _D) for Delta Chains.

    • Single-Domain / Single-Chain: Append _HC, _VHH, or upload standalone single-chain records (VHH, scFv, single-chain TCR).

  • CSV Sequence Format (name,seq1,seq2): For CSV files, format each entry with three comma-separated columns: name,seq1,seq2 (headers such as Name,Sequence1,Sequence2 or Name,HC,LC are optional). The system automatically evaluates seq1 and seq2 using sequence annotation models to determine chain assignments.

Example (Antibody FASTA): 

>Ab001_LC
ESALTQPASVSGSPGQSITI...
>Ab001_HC
EVQLVQSGAEVKKPGASVKV...

Example (TCR FASTA): 

>TCR01_TRA
QSVTQPDARVTVSEGASLQL...
>TCR01_TRB
EAAVTQSPRNKVAVTGGKVT...

Example (CSV): 

name,seq1,seq2
Ab001,EVQLVQSGAEVKKPGASVKV...,ESALTQPASVSGSPGQSITI...
Ab002,DIQMTQSPSSLSASVGDRVT...,EVQLVESGGGLVQPGGSLRL...

Structure Association Logic (PDB & mmCIF)

AbLead automatically associates optionally uploaded or built structure files (PDB or mmCIF) with your Fv sequences based on exact name matching.

  • Rule: If an Fv sequence has the basename Ab001, the system looks for an associated structure file named Ab001.pdb, Ab001.cif, or Ab001.mmcif in your uploaded files.
  • Effect: If a match is found, structural surface properties (SPH, SPP, SPN, SPCD) are calculated. If not, only sequence-based metrics are reported. The associated structure file is also used in the Liabilities analysis.
  • Chain Labels: The structure file should contain both chains, with the Light Chain labeled L and the Heavy Chain labeled H. This is required for the Liabilities analysis.

[!NOTE] Format Normalization & Multi-File Upload: To ensure consistent analysis and visualization across the platform, sequence imports in non-FASTA or tabular formats (such as CSV, GenBank, EMBL, SwissProt, or Clustal) are automatically parsed and converted to FASTA format upon upload (with CSV sequence pairs automatically classified into Heavy and Light chains). Multiple sequence files can be selected and uploaded at the same time; the system automatically merges and parses all entries into a unified dataset. Similarly, all uploaded structure files (including .cif and .mmcif models) are automatically converted and saved to the database in standard PDB format.

Run Analysis

Clicking Run Analysis will run the analysis on the project. Upon completion, the Project View may be displayed, or the dialog may be closed to return to the Dashboard.

Project Sharing

Projects can be shared with other users within the same organization (same company or email domain) on the system directly from the Project View. If you have the appropriate permissions, clicking Share will open a dialog allowing you to add users by email and define their access level:

  • Read-Only: Shared users can view all project data, run analyses that do not save data (like exporting or viewing variants), but they cannot save any modifications, apply mutations, or delete the project.
  • Write: Shared users have full modification permissions to edit, engineer, and apply mutations to the project.
  • Grant: Shared users can additionally share the project with others and manage their permissions.

Export/Import Project (.zip)

A project or group of projects may be exported to a .zip file from the main Dashboard by clicking File > Export Project (or from within the Project View under Export > Export Project (.zip)). This creates a standalone .zip archive containing the project name, notes, custom columns schema, all sequences, attached PDB structure files, and pre-calculated analysis results. For detailed information on the archive bundle contents, see the Export Project (.zip) documentation.

An exported project or group of projects may be imported by clicking File > Import Project (.zip). This will open a dialog allowing you to select a .zip file to import. The project or projects will be imported into the Dashboard of the current user with all data and analysis results intact. This feature allows for offline project sharing, backups, or storage.

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Import Library & Saved Library Runs

Sequence files (supporting FASTQ, FASTA, GenBank, EMBL, SwissProt, Clustal, and multi-file .zip/.gz archives) containing nucleotide or protein sequences can be evaluated, quality-controlled, permanently saved, and selectively imported into projects using the Import Library workspace tool.

For a comprehensive guide covering Phred quality scores, 7-region IMGT domain completeness checks, N-terminal framework integrity, clonal abundance tracking, singleton noise filtering, plate map demultiplexing, and visual analytics, see the dedicated Library Evaluation & Import documentation.

  1. Navigate to the Dashboard.

  2. Click File > Import Library.

  3. Enter a Library / Project Name and select the Expected Format (scFv, VHH, Paired Fv, Fab, or Auto-detect).

  4. Upload one or more .fastq, .fasta, .zip, or .gz files (or paste raw sequences), optionally accompanied by a plate map CSV or TSV file for barcode and well demultiplexing.

  5. Click Validate Library to begin real-time streaming translation, domain quality control, and clonal deduplication. If anomalies are detected in an uploaded plate map (such as leading delimiter rows from spreadsheet exports or barcode kit mismatches), an interactive pre-import warning modal alerts you before large sequencing archives upload, offering options to auto-trim blank rows, cancel, or proceed.

  6. In-Database Persistence: Once evaluated, the entire library run (summary metrics, QC distributions, interactive charts, demultiplexing summaries, and evaluated clone sequences) is automatically and permanently saved to the database as a Library Project, while temporary raw sequencing files are immediately discarded to keep storage lightweight.

  7. Use the Status Filter (Productive, Valid Only, Warnings Only, Non-Productive Only), Import Status Filter (All Clones, Not Yet Imported, Already Imported), Hide Singletons (≥2 reads) toggle, and Min Frequency (%) inputs to isolate true enriched clones from sequencing noise.

  8. Clonal Import Lineage & Project Harvesting: Select desired candidate clones and click Import Selected to Project. Choose between appending candidates to an existing project or creating a new project. When a new project is created, the dialog automatically defaults to that new project for all subsequent clone selections without requiring a page reload. Harvested clones are marked with a green Imported badge with hover tooltips detailing destination project names and timestamps. Tracking is keyed strictly to unique clone and well identifiers, allowing duplicate binders across different physical wells to be imported independently without lineage collisions.

  9. Dashboard Management: Evaluated libraries appear directly in your Dashboard under the Libraries grid (or combined in All Items). Click any library title or row to reopen the full evaluation session with all filters, charts, and import lineage indicators intact.

Note: Preprocessing raw next-generation sequencing data is outside the scope of a developability and engineering dashboard like AbLead. Before uploading files to AbLead, users should run their raw sequencer outputs through standard upstream bioinformatics pipelines to:

  • Trim Adapters & Quality Filter: Remove low-quality bases and sequencing adapters (using tools like Cutadapt or Trimmomatic).

  • Merge Overlapping Reads: Align and merge R1 and R2 into a single full-length read (using standard assemblers like PEAR, FLASH, or Pandaseq).

  • Isolate Fv/VHH regions: Trim constant regions or primer sequences if necessary.

Deleting and Restoring Projects & Libraries

Clicking File > Delete Selected (or pressing the trash icon button in the toolbar) soft-deletes selected projects, libraries, or mixed selections and moves them into the Trash.

Clicking File > Trash opens the Trash management view where items can be restored to the active Dashboard or permanently purged:

  • Restoring: Select projects or libraries and click Restore Selected (or use the individual restore action) to return items to the active Dashboard with all sequences, analysis results, and labels intact.

  • Permanent Deletion: Select items and click Delete Selected to permanently purge them from the database, or click Empty Trash to purge all deleted items.

Dashboard Views, Shared Labels & Archiving

The collapsible pancake menu sidebar (\(\equiv\)) provides streamlined workspace navigation organized into Views and Labels.

Dashboard Views

The Views section provides instantaneous access to 5 standard operational views with live count badges:

  • Active Projects (#): The primary project working view (similar to an Inbox). Displays all active projects currently tagged with the Active Projects system label.

  • All Projects (#): Displays all non-deleted projects belonging to or shared with you, regardless of archived or label status.

  • Active Libraries (#): Displays all active, non-archived saved library evaluation runs.

  • All Libraries (#): Displays all evaluated library runs saved in your account.

  • All Items (#): Presents both projects and libraries in unified, parallel management grids for cross-cutting oversight.

Shared Labels Across Projects & Libraries

Labels enable hierarchical grouping and category tagging across both Projects and Libraries interchangeably:

  • Creating Labels: Click Labels > New Label (or the plus icon in the sidebar) to create new custom labels and define optional parent-child nesting relationships.

  • Managing Labels: Click Labels > Manage Labels (or the gear icon in the sidebar) to organize, rename, or delete existing user labels.

  • Applying Labels: Select one or more projects, libraries, or mixed items in the dashboard grids and click Apply Labels... in the bulk action bar. A tri-state dropdown reflects the shared label state (on, mixed, off) across all selected items, allowing you to add or remove labels in a single transaction.

  • Filtering by Label: Clicking any label in the sidebar label tree filters the active view in place without redirecting or switching away from your current projects, libraries, or all items context.

  • Visual Badges: Both projects and libraries display colored label badge pills in a dedicated Labels column. Table headers and cells maintain fixed single-line widths that slide horizontally with container scrolling when the sidebar expands, and support interactive drag-resizing.

Archiving and Unarchiving

  • Archiving: Selecting one or more items in an active view reveals the Archive button ( Archive) in the bulk action bar. Clicking Archive removes the Active Projects system label from the selected projects or libraries, moving them out of active views while keeping all data intact.

  • Unarchiving: Selecting items while in an "All" view displays the Unarchive button ( Unarchive). Clicking Unarchive restores the Active Projects label, returning them to the active working views.

Global Projects

Global (or Public) Projects are administrator-managed reference projects made available system-wide to all registered users across all domains:

  • Identification: Global projects are marked with a blue Global badge on the main dashboard project list.

  • Access Level: Non-administrator users have Read-Only access to Global projects, allowing complete dataset inspection, visualization, sequence comparison, and data exports without modifying master records.

  • Copy Projects: Users may copy Global projects to their own Dashboard for modification by selecting the Global project(s) and using File > Export Project (.zip). Then click File > Import Project (.zip) and import the exported project(s).

Project Names and Notes

Projects and libraries without existing notes display an italicized + Add notes... placeholder. Double-click empty space in a project name field or anywhere in a notes cell to edit names and notes inline. Edits are saved automatically upon pressing Enter or clicking outside the field.

Searching Projects and Entries

The Dashboard search bar allows finding projects and individual antibody entries across all areas or limited to specific attributes such as names, notes, labels, sequence regions, germlines, or metadata values. Additionally, a project-level search bar is available directly inside the Project View's inner toolbar to filter the results table dynamically using the exact same options:

  • Standard Search: Enter any name, note substring, label, or sequence subsequence (e.g., EVQLV) to find matching records across all areas.

  • Area Filters: Use the Area Filter dropdown selector on the search bar or specify a search prefix to limit your query to specific data fields:

    • name:<query>: Searches both project names and antibody/entry names.
    • project:<query>: Searches project names only.
    • entry:<query>: Searches antibody/entry names only.
    • notes:<query>: Searches project notes and entry engineering notes.
    • label:<query>: Searches project labels.
    • seq:<query>: Searches heavy and light chain amino acid sequences (including PROSITE motifs and domain scopes).
    • germline:<query>: Searches germline origin annotations (species, V-gene, J-gene, leader, constant domain).
    • meta:<query>: Searches custom metadata columns and results values.

  • PROSITE Motif Search: Enter NCBI/PROSITE regular expression motifs (e.g., N{P}[ST]{P}) to scan sequences for complex patterns.

  • Domain Modifiers: Appending a suffix scope restricts sequence searches to specific regions:

    • .Fv: Restricts sequence search to both variable domains (Variable Heavy + Variable Light).
    • .VH: Restricts sequence search to the Variable Heavy domain only.
    • .VL: Restricts sequence search to the Variable Light domain only.

Example: Searching for seq:N{P}[ST].VH or name:Trastuzumab will find exact matches scoped strictly to the selected attribute.

Dashboard Table Filtering and Multi-Column Sorting

Both the Projects and Libraries tables on the Dashboard support centralized interactive filtering and multi-column sorting:

  • Multi-Column Sorting: Click any sortable column header to cycle through Ascending, Descending, and Unsorted orders:

    • Projects Table Columns: Project ID and Name, Labels, Notes, Date Created, Date Run, Fv Count, PDB Count, and Analysis Status.

    • Libraries Table Columns: Library ID and Name, Labels, Notes, Date Created, Format, Total Reads, Unique Clones, QC Breakdown, and Harvested.

    Clicking additional headers adds secondary and tertiary tiebreakers to a composite sort stack. Directional arrows and numerical rank badges indicate the relative priority of each active sort.

  • Column Filtering with Google-Norm Negation: Click the filter funnel icon () in any column header to open the quick-filter popover:

    • Negation Search: Prefix any term with a hyphen (-) or NOT (e.g. -Variant or NOT Complete) to exclude matching projects or libraries.

    • Quoted Exact Matches: Enclose queries in quotation marks (e.g. "-rhesus" or "Variant Study") to search for literal strings containing hyphens or spaces.

    • Relational Comparisons: Filter numeric columns (such as Fv Count, PDB Count, Total Reads, Unique Clones, or Harvested) using mathematical operators (>10, <=5, <20, >=50, or =0).

    • Numeric Ranges: Enter numerical ranges (e.g. 10-50 or 1000-50000) to isolate records with counts within specific intervals.

    • Comma-Separated Multi-Term Lists: Supply multiple comma-separated terms (e.g. Oncology, Preclinical, -Diagnostic) to combine OR inclusion logic with AND exclusion rules.

  • Dedicated Notes Column for Libraries: The Libraries table features a standalone, sortable, and filterable Notes column with inline double-click editing, separating engineering and library notes from library names.

  • Active Filters and Sorts Bar: Interactive status bars above both tables display clickable filter and sort chips, live count summaries (e.g. Showing 3 of 12 projects or Showing 2 of 5 libraries), and a single-click Clear All button to reset all active filters and sorts.

  • Session Persistence: Active sorts and column filters persist across page reloads and tab navigations within the user session for both projects and libraries.

Logout

Clicking File > Logout will log you out of the application.