Tool Catalog
Every computational surface in NextELN carries a maturity label so you can tell what is validated, what is in evaluation, and what is a research prototype or educational analysis. The definitions are:
| Status | Meaning |
|---|---|
| Production | Available and operational for customers. |
| Beta | Available but still under evaluation. |
| Research preview | Prototype, not validated for routine use. Outputs are hypotheses. |
| Roadmap | Planned, not yet implemented. |
| Literature review | Educational analysis, not a product. |
Catalog
| Tool | Surface | Maturity | Notes |
|---|---|---|---|
| Sequence Toolkit | In-app (/eln/tools) |
Production | Reverse-complement, translation, ORF, GC/Tm, protein properties. Deterministic. |
| Pairwise Alignment | In-app | Production | Needleman–Wunsch / Smith–Waterman + BLOSUM62. |
| Gene-Set Enrichment (ORA) | In-app | Production | Hypergeometric ORA + Benjamini–Hochberg FDR. |
| CRISPR gRNA Design | In-app | Production | PAM scan + on-target guide ranking. |
| Restriction & Cloning Planner | In-app | Production | Restriction maps + digest fragments. |
| PCR Primer Design | In-app | Production | Forward/reverse pair at a target Tm. |
| Motif / Pattern Search | In-app | Production | IUPAC / PROSITE search, both strands. |
| Phylogenetic Tree | In-app | Production | Alignment-free UPGMA from k-mer distances. |
| Codon Usage & Optimization | In-app | Production | Human CAI, rare codons, back-translation. |
| Sequence Format Converter | In-app | Production | FASTA/GenBank/tabular/raw interconversion. |
| FASTQ Quality Control | In-app | Production | Per-cycle quality, Q20/Q30, GC, N content. |
| Protein Hydropathy Profiler | In-app | Production | Kyte–Doolittle + net charge, TM spans. |
| 3D Protein Structure Viewer | In-app + GPU | Beta | ESMFold fold / PDB / AlphaFold pull, pLDDT coloring. Benchmarking in progress. |
| Antigenic Peptide Finder | In-app + GPU | Beta | Ranked immunogenic peptides; retrospective validation ongoing. |
| Nanobody Variant Prioritizer | In-app | Research preview | Auditable, framework-preserving CDR3 candidate ranking. Not an affinity predictor. |
| mRNA Vaccine Candidate Designer | In-app + GPU | Research preview | Candidate package for expert review and preclinical validation — not a bench-ready vaccine. |
| Bispecific Antibody Development | Research note | Literature review | Domain review and proposed design-build-test-learn workflow; no design engine yet. |
| Bioinformatics tools in the AI era | Research note | Literature review | 2,485-paper CPU/GPU survey; a planning framework, not a tool. |
| Frontier generative design (RFdiffusion, ProteinMPNN, AlphaFold-Multimer, Boltz) | GPU tier | Roadmap | Planned adapters on the self-hosted bio-inference service. |
How to read this
- Production / Beta tools can be used in real work today. Beta outputs should still be reviewed and, where stakes are high, confirmed against a reference.
- Research preview tools generate candidate hypotheses. Treat their ranked outputs as inputs to human review, structure-level computation, and experimental validation — never as predictions of binding, efficacy, or safety.
- Literature review pages are educational. They describe the state of the field and our intended approach; they are not claims that a working product exists.
- Roadmap items are not yet available.
Model licensing
Before any model-backed step is offered as a commercial hosted service, its license is recorded in our model registry (software license, model-weight license, commercial-use status, redistribution rights, required citations). Notably: NetMHCpan requires a commercial license outside publicly-funded academic use, and AlphaFold 3 weights carry non-commercial restrictions, while AlphaFold 2 and ESMFold are more permissively licensed. "Published" does not automatically mean "permitted as a commercial hosted service."
Research-note tools are prepared with the NextELN AI Lab Assistant and scientifically reviewed by the NextELN science team, Excellgen, Inc.