SmarLens

Beta

SmarLens is a web-based genomics workspace for milk thistle (Silybum marianum), built to support gene-centered exploration of the chromosome-level genome assembly and annotation reported by Kim et al., 2024. The current beta provides Smar gene lookup, transcript model visualization, sequence context, expression summaries, protein domain inspection, and similarity analysis against Arabidopsis resources.

About SmarLens

SmarLens is a beta-stage genomics workspace for gene-centered exploration of milk thistle (Silybum marianum).

Purpose

SmarLens was developed to make early milk thistle genome resources easier to search, inspect, and connect to functional hypotheses. The current release focuses on practical access to Smar gene identifiers, transcript structures, genomic sequence context, expression profiles, protein domains, and similarity relationships with Arabidopsis protein resources.

Reference Genome And Annotation

The genome assembly and annotation used by SmarLens are based on Chromosome-level genome assembly of milk thistle (Silybum marianum (L.) Gaertn.). Public source files are available from the associated figshare dataset.

Current Scope

This beta version provides gene search, multi-gene summaries, transcript model rendering, sequence visualization with flanking controls, normalized RNA-seq count summaries, Pfam-based protein domain views, Arabidopsis similarity candidates, and phylogenetic tree rendering. Download and documentation pages are planned but not yet implemented.

Public Test Limits

For public beta testing, SmarLens currently accepts up to 10 query terms per request. Heavy analyses such as BLAST, hmmscan, MAFFT, and FastTree are timeout-limited and run with restricted concurrency to protect server availability.

Disclaimer

SmarLens is provided as a research-oriented beta resource. The developers and affiliated laboratory do not warrant, and do not assume legal liability or responsibility for, the accuracy, completeness, or usefulness of any data, analysis result, annotation, software output, document, or related information made available through this tool.

Development Team

Main Developer and Code Architect

Janghyun Choi, Ph.D.

Implemented the main pipeline modules and designed the major functional components of SmarLens.

Project Supervisors

Janghyun Choi, Ph.D.

Jinmi Yoon, Ph.D.

Provided conceptual guidance and overall project supervision.

Contributor

Sinhoe Ahn

Contributed to code implementation, module development, pipeline testing, data processing, logic refinement, and validation.

Maintenance

Pipeline maintained by Janghyun Choi · jchoi@inha.ac.kr

Source Code

Source code and issue tracking are available on GitHub.