Genomics Proteomics Metagenomics Visualization

Bioinformatics Workbench — an online laboratory for exploring biological data

Analysis, simulation, educational pathways, collaborations with labs, AI assistant for genomics, proteomics, metagenomics. For students, researchers, teachers, biotech companies.

110+

Ready pipelines and simulations

24/7

Access to cloud computing and GPU

65%

Time savings from automation

40

Partner laboratories and R&D facilities

Work Environment Modules

Modules can be combined, run pipelines, and collaborate in real time.

  • ✅ Sequence Analysis: QC, alignment, variant calling, annotation.
  • ✅ Transcriptomics & Proteomics: differential expression, pathway analysis, network biology.
  • ✅ Metagenomics: taxonomic profiling, functional analysis, microbiome dashboards.
  • ✅ Structural Biology: 3D modeling, docking, visualization.

Tools & integrations

Bioinformatics Stack

Jupyter, Galaxy, Nextflow, Snakemake, RStudio, Bioconductor.

AI Assistant

AUTOMATION, EXPLAINABLE RECOMMENDATIONS, ANOMALY DETECTION.

Data Sources

NCBI, ENA, UCSC, PDB, ClinVar, GTEx, custom data lakes, LIMS.

Collaboration

Shared workspace, version control, DOIs, live comments, review.

Learning and pathway

Student & Educator Pathway

  • 🎓 Courses on bioinformatics basics, lab work, simulations.
  • 📚 Lesson plans, assessment,  integration with LMS.
  • 📜 Bioinformatics Explorer certifications, Educator PD credits.

Research & Clinical Pathway

  • 🧪 Pipelines for clinical diagnostics, pharmacy, biotech.
  • 🔬 Preparation for CLIA, ISO, GxP Accreditation
  • 🤝 Collaboration with labs, grants, publications.

Industry & Startups

  • 💼 Product Analytics, R&D, Automation, Compliance.
  • 📈 Pitch Templates, Roadmaps, Investor Reports.
  • 🤝 Accelerator, mentoring, access to data & partners.

Entry: Revolution in bioinformatics in the era of big data

Bioinformatics has become a critically important field at the intersection of biology, computer science, and mathematics. With the advent of high-throughput sequencing (NGS) technologies, the volume of genomic data is growing exponentially—over 100 petabytes of biological data are generated annually. Bioinformatics Workbench was created as a comprehensive platform for analyzing these massive datasets, combining powerful computational tools, intelligent automation, and intuitive interfaces.

The platform provides access to the full spectrum of bioinformatics methods: from basic sequencing operations to complex multi-omics analyses, from genomic annotations to proteomic profiling, from structural biology to systems biology. We integrate the best open tools (Galaxy, Nextflow, Bioconductor), cloud computing resources, and AI assistants for automating routine tasks and generating insights.

Bioinformatics Workbench simplifies complex analyses, making them accessible to students, researchers, and clinicians without deep technical knowledge. Through visual pipeline builders, ready workflows, and interactive tutorials, users can quickly learn and apply sophisticated methods. The system automatically generates reports, visualizations, and recommendations, saving time and ensuring quality results.

Deep functional module analysis

Sequence Analysis: from raw data to biological insights

Module sequence analysis provides a full data sequencing pipeline:

  • Quality Control (QC): AUTOMATIC QUALITY ASSESSMENT USING FastQC, MultiQC. ADAPTER CONTAMINATION, PCR DUPLICATES, LOW-QUALITY READS DETECTION. VISUALIZATION OF QUALITY METRICS AND AUTOMATED FILTERING RECOMMENDATIONS.
  • Alignment & Assembly: ALIGNMENT TO REFERENCE GENOMES (BWA, Bowtie2, STAR) OR DE NOVO ASSEMBLY (SPAdes, Canu, Flye). OPTIMIZATION OF PARAMETERS FOR VARIOUS DATA TYPES (SHORT-READ, LONG-READ, HYBRID).
  • Variant Calling: SNP, INDEL DETECTION (GATK, FreeBayes, VarScan). FILTERING AND ANNOTATION OF VARIANTS THROUGH DATABASES (dbSNP, ClinVar, gnomAD).
  • Annotation:Functional annotation of genes and variants via databases (GO, KEGG, Reactome). Predicting variant effects on proteins (SIFT, PolyPhen, CADD).

Transcriptomics & Proteomics: systems view of expression

Modules of transcriptomics and proteomics allow analyzing gene and protein expression:

  • Differential Expression: DIFFERENTIAL EXPRESSION ANALYSIS OF GENES/PROTEINS BETWEEN CONDITIONS (DESeq2, edgeR, limma). STATISTICAL TESTS WITH MULTIPLE TESTING CORRECTION (FDR, Bonferroni).
  • Pathway Analysis:Enrichment analysis for functional pathways (GSEA, ORA, pathway topology). Integration with pathway databases (KEGG, Reactome, WikiPathways).
  • Network Biology:Building and analyzing biological networks (protein-protein interactions, gene regulatory networks). Identifying hub genes and modules through community detection algorithms.

Content hub and SEO resources

Knowledge library

Syndicate content across more than 400 educational modules, thematic labs, and simulations. Each article is optimized for feature snippets with cross-language translations in 66 languages.

  • Trending queries sections: CRISPR, single-cell, spatial omics, vaccinology.
  • Constructor for long-form guides with templates for journals and open courses.
  • Marketing Team Modules: keyword clusters, schema markup, metadata.

Regulatory packages

Ensure compliance in research: GDPR, HIPAA, DUA, data licenses. The portal generates policy briefs, data-sharing agreements, IRB/IEC checklists.

  • Country profiles with local requirements, data export procedures.
  • AUTOMATIC REPORTS FOR GRANT SUBMISSIONS, CLINICAL TRIALS, DATA STewardSHIP.
  • Integration with ELN/LIMS for tracking dataset origin and usage.

Community development

Launch community programs: workshops, hackathons, newsletter, podcasts. Get KPIs on engagement, leads, partnerships, citation of research.

  • Editorial calendar with ready series, email nurturing, social campaigns.
  • Mentorship platform: mentor profiles, matching, progress, certificates.
  • SEO integration: hreflang management, schema Dataset/ScholarlyArticle, RSS.

FAQ — 10 questions

Do powerful local resources have to be used?➕
No, the platform uses cloud GPUs/CSPs. Available quotas, auto-scaling, cost control.
Can we import our data?➕
Yes, through S3, Google Cloud, Azure Blob, SFTP, API, local upload. Supported are standard formats FASTQ, BAM, VCF, mzML, CSV.
How is safety assured?➕
Encryption, role-based access, audit, GDPR/HIPAA compliance, private instances, isolated environments.
Is there visualization of results?➕
Yes, interactive heatmaps, volcano plots, pathway maps, 3D structures, integration with Tableau/Power BI.
How does the AI assistant work?➕
AI proposes pipelines, checks quality, explains results, generates reports, suggests literature.
Are common workspaces provided?➕
Yes, create collaborative workspaces with access control, change history, version control, comments.
Can we run educational workshops?➕
Platform includes instructor mode, demo datasets, interactive demonstrations, assessment, badges.
How to prepare for certifications?➕
Pathway assist in preparing for ISTQB Bioinformatics, AMIA, Coursera/edX, Science Portal certifications.
Is integration with laboratory equipment supported?➕
Yes, through LIMS, ELN, API for sequencers, spectrometers, IoT sensors.
Is there a library of educational materials?➕
YES, videos, articles, case studies, interactive simulations, terminology dictionary, Q&A forum.