Translation Diff Export
Devolutions/UniGetUI
Compares UniGetUI JSON locale files against English, identifies untranslated or source-changed keys, and generates patch, reference, and handoff files for a target language.
Map translation initiation sites, including non-AUG and alternative starts, from initiation-drug ribosome profiling (TI-seq).
$ npx skills add GPTomics/bioSkills --skill bio-ribo-seq-initiation-site-mapping -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install GPTomics/bioSkills bio-ribo-seq-initiation-site-mapping --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/GPTomics/bioSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/ribo-seq/initiation-site-mapping .claude/skills/bio-ribo-seq-initiation-site-mapping && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "bio-ribo-seq-initiation-site-mapping" agent skill from https://github.com/GPTomics/bioSkills/tree/main/ribo-seq/initiation-site-mapping into .claude/skills/bio-ribo-seq-initiation-site-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-ribo-seq-initiation-site-mapping", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/GPTomics/bioSkills/tree/main/ribo-seq/initiation-site-mappingType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add GPTomics/bioSkills --skill bio-ribo-seq-initiation-site-mapping -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install GPTomics/bioSkills bio-ribo-seq-initiation-site-mapping --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/GPTomics/bioSkills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/ribo-seq/initiation-site-mapping .agents/skills/bio-ribo-seq-initiation-site-mapping && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-ribo-seq-initiation-site-mapping" agent skill from https://github.com/GPTomics/bioSkills/tree/main/ribo-seq/initiation-site-mapping into .agents/skills/bio-ribo-seq-initiation-site-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-ribo-seq-initiation-site-mapping", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add GPTomics/bioSkills --skill bio-ribo-seq-initiation-site-mapping -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install GPTomics/bioSkills bio-ribo-seq-initiation-site-mapping --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/GPTomics/bioSkills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/ribo-seq/initiation-site-mapping .cursor/skills/bio-ribo-seq-initiation-site-mapping && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "bio-ribo-seq-initiation-site-mapping" agent skill from https://github.com/GPTomics/bioSkills/tree/main/ribo-seq/initiation-site-mapping into .cursor/skills/bio-ribo-seq-initiation-site-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-ribo-seq-initiation-site-mapping", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/GPTomics/bioSkills.git --path ribo-seq/initiation-site-mapping--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add GPTomics/bioSkills --skill bio-ribo-seq-initiation-site-mapping -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install GPTomics/bioSkills bio-ribo-seq-initiation-site-mapping --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/GPTomics/bioSkills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/ribo-seq/initiation-site-mapping .gemini/skills/bio-ribo-seq-initiation-site-mapping && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "bio-ribo-seq-initiation-site-mapping" agent skill from https://github.com/GPTomics/bioSkills/tree/main/ribo-seq/initiation-site-mapping into .gemini/skills/bio-ribo-seq-initiation-site-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-ribo-seq-initiation-site-mapping", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install GPTomics/bioSkills bio-ribo-seq-initiation-site-mappingInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add GPTomics/bioSkills --skill bio-ribo-seq-initiation-site-mapping -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/GPTomics/bioSkills.git skills-src && mkdir -p .github/skills && cp -r skills-src/ribo-seq/initiation-site-mapping .github/skills/bio-ribo-seq-initiation-site-mapping && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "bio-ribo-seq-initiation-site-mapping" agent skill from https://github.com/GPTomics/bioSkills/tree/main/ribo-seq/initiation-site-mapping into .github/skills/bio-ribo-seq-initiation-site-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-ribo-seq-initiation-site-mapping", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add GPTomics/bioSkills --skill bio-ribo-seq-initiation-site-mapping -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install GPTomics/bioSkills bio-ribo-seq-initiation-site-mapping --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/GPTomics/bioSkills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/ribo-seq/initiation-site-mapping .opencode/skills/bio-ribo-seq-initiation-site-mapping && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "bio-ribo-seq-initiation-site-mapping" agent skill from https://github.com/GPTomics/bioSkills/tree/main/ribo-seq/initiation-site-mapping into .opencode/skills/bio-ribo-seq-initiation-site-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-ribo-seq-initiation-site-mapping", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
bio-ribo-seq-initiation-site-mappingMap translation initiation sites, including non-AUG and alternative starts, from initiation-drug ribosome profiling (TI-seq).
Bio Ribo Seq Initiation Site Mapping is an agent skill from GPTomics/bioSkills. Map translation initiation sites, including non-AUG and alternative starts, from initiation-drug ribosome profiling (TI-seq). Use when locating start codons, detecting near-cognate or upstream initiation, or analyzing harringtonine, lactimidomycin (GTI-seq/QTI-seq), or retapamulin (Ribo-RET) data.
Its SKILL.md is about 2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/map_initiation_sites.sh` and `usage-guide.md`).
It sits in Writing & Content, covering Translation. The repository describes itself as: a set of SKILLS.md for doing bioinformatics with agents like claude code. The licence is MIT.
Read from SKILL.md and the folder at commit d91ed3d. It shows what the files ask for, not the result of running them.
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Ships script files (Shell), which the agent can run.
Shell commands in SKILL.md call:
pipFrom the folder's file list and the shell code blocks in SKILL.md.
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Bio Ribo Seq Initiation Site Mapping loads about 2k tokens when it runs. Until then it costs about 84 tokens; SKILL.md has 899 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
The full file from GPTomics/bioSkills at commit d91ed3d, republished under its MIT licence (© GPTomics). 899 words, ~1,999 tokens.
.claude/skills/bio-ribo-seq-initiation-site-mapping/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.Reference examples tested with: Ribo-TISH 0.2.7+, PRICE/GEDI 1.0.5+, samtools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
<tool> --version then <tool> --help to confirm flagspip show <package> then help(module.function) to check signaturesIf code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
"Map where translation starts in my Ribo-seq data" -> Locate translation initiation sites (TIS) at single-nucleotide resolution, including non-AUG and upstream starts, from initiation-drug profiling experiments.
Ribo-TISH for TIS detection from harringtonine/LTM data; PRICE for EM-based cryptic-start detectionThis is a distinct analysis from elongation ORF detection: it asks WHERE initiation occurs (which start codon), not which ORF bodies are translated. It typically requires a dedicated initiation-drug library paired with a standard elongation library.
| Method | Drug(s) | Signal | Citation |
|---|---|---|---|
| Harringtonine TIS | harringtonine | binds free 60S, blocks the first peptide bond; broad start peak | Ingolia 2011 |
| GTI-seq | lactimidomycin (LTM) + CHX in parallel | LTM blocks translocation at the assembled 80S; sharp start peak | Lee 2012 |
| QTI-seq | LTM then puromycin (sequential) | puromycin strips elongating ribosomes; quantitative, low background | Gao 2015 |
| Ribo-RET (bacteria) | retapamulin | arrests initiating 70S at start codons | Meydan 2019 |
All three drugs CREATE the initiation signal by halting or removing elongation; the data is a deliberate artifact read out at the start codon. LTM gives sharper peaks than harringtonine because it cannot act on elongating ribosomes whose E-site is occupied. QTI-seq (LTM then puromycin) is analyzed on the same LTM path below; the puromycin step only strips elongating ribosomes to lower the background, so the TIS library is still passed as the LTM-type -t input. Without an initiation-drug library, start codons can only be inferred indirectly from elongation periodicity (see orf-detection).
Initiation occurs at AUG and near-cognate codons differing by one base; the biologically used set is CUG, GUG, ACG, UUG, AUU, AUC, AUA (AAG/AGG also differ by one base but initiate negligibly). CUG is the dominant near-cognate start (~16% of mapped sites in GTI-seq; AUG remains >50%). uORFs especially use near-cognate starts, so initiation mapping must enable alternative start codons to recover them; an AUG-only search misses most upstream initiation.
| Situation | Tool | Why |
|---|---|---|
| TIS from harringtonine/LTM data, with QC | Ribo-TISH | quality + predict modes; near-cognate via --alt; differential TIS |
| Cryptic/near-cognate starts, EM model | PRICE | per-codon EM; handles near-cognate; designed for cryptic events |
| Bacterial initiation (Ribo-RET) | dedicated retapamulin analysis | prokaryote initiation; eukaryote periodicity tools fit poorly |
Goal: Confirm the drug enriched start-codon signal and pick P-site offsets before predicting.
Approach: Run Ribo-TISH quality, which reports the metagene profile and writes a per-length offset parameter file.
# Writes a <ribo.bam>.para.py offset file and a QC figure
ribotish quality -b ribo_elongation.bam -g annotation.gtf -o ribo_quality.txt -f ribo_qc.pdf
ribotish quality -b ribo_tis.bam -g annotation.gtf -o tis_quality.txt -f tis_qc.pdfGoal: Call TIS, including non-AUG starts, using the initiation-drug library.
Approach: Run ribotish predict with the elongation BAM (-b) and the TIS/harringtonine/LTM BAM (-t), enabling alternative start codons.
# --harr marks the TIS library as harringtonine-type; --alt enables near-cognate starts
ribotish predict \
-b ribo_elongation.bam \
-t ribo_tis.bam \
-g annotation.gtf \
-f genome.fa \
--harr --harrwidth 15 --alt \
-o tis_predictions.txtThe output lists initiation sites with the start codon, ORF type, and significance. For differential initiation across conditions, ribotish tisdiff compares two TIS libraries.
Goal: Detect cryptic and near-cognate initiation with an EM model.
Approach: Prepare the genome and run the Price tool in GEDI on the Ribo-seq reads.
gedi -e Price -reads ribo_elongation.bam -genomic prepared_genome -prefix price_outPRICE reports a per-ORF p-value from a generalized binomial model (not multiple-testing corrected); codon-level activity is written to price_out.codons.cit.
A called TIS is strongest when it shows a sharp drug-induced start peak, a downstream in-frame elongation signal in the standard library, and (for novel sites) conservation or peptide support. Alternative N-terminal starts and uORF starts frequently use near-cognate codons; report the start codon identity, not just the position. Initiation at a uORF does not guarantee a stable protein product (see orf-detection validation).
| Symptom | Cause | Fix |
|---|---|---|
| Only AUG starts found | Alternative starts not enabled | Add --alt (Ribo-TISH) or use PRICE for near-cognate |
| Broad, smeared start peaks | Harringtonine data treated as sharp LTM data | Use --harr; expect broader peaks than LTM |
predict gives weak calls | Missing the paired elongation BAM (-b) | Provide both -b (elongation) and -t (TIS) libraries |
| TIS analysis on elongation-only data | No initiation-drug library present | Initiation mapping needs harringtonine/LTM/RET data; otherwise infer from periodicity |
| Bacterial data mis-called | Eukaryote TIS tool on Ribo-RET data | Use a retapamulin/prokaryote initiation workflow |
© GPTomics, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
SKILL.md and 2 other files in ribo-seq/initiation-site-mapping of GPTomics/bioSkills.
Open the folder on GitHubat commit d91ed3d
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in GPTomics/bioSkills, which our catalogue first saw on October 7, 2026.
Bio Ribo Seq Initiation Site Mapping next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Bio Ribo Seq Initiation Site Mapping this skillGPTomics/bioSkills | 1.2k | 1 repos | ~2k | Automated safety check: Pass | MIT | |
| Translation Diff ExportDevolutions/UniGetUI | 26k | — | ~1.1k | Automated safety check: Pass | MIT | |
| Sync Translationssymfony/symfony | 31k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Translation Diff ImportDevolutions/UniGetUI | 26k | — | ~750 | Automated safety check: Pass | MIT | |
| Translation Diff TranslateDevolutions/UniGetUI | 26k | — | ~934 | Automated safety check: Pass | MIT | |
| Generate Translationspayloadcms/payload | 45k | — | ~1.1k | Automated safety check: Pass | MIT |
Devolutions/UniGetUI
Compares UniGetUI JSON locale files against English, identifies untranslated or source-changed keys, and generates patch, reference, and handoff files for a target language.
symfony/symfony
Synchronize translation catalogs across maintained Symfony branches: find messages that newer branches added to the English catalogs but that are still missing from the oldest maintained branch…
Devolutions/UniGetUI
Merges translated key-value pairs from a UniGetUI JSON localization patch back into the full language file and validates the merged result.
Devolutions/UniGetUI
Translates a sparse UniGetUI JSON language patch, writes completed entries into the working copy, preserves placeholders and terminology, and prepares the patch for merge-back.
payloadcms/payload
A skill your agent uses when new translation keys are added to packages to generate new translations strings
Narcooo/inkos
Drives long-form fiction, scripts, storyboards, interactive films and long-document translation through InkOS, with every change made by a typed action.
GPTomics/bioSkills
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO.
GPTomics/bioSkills
Installs the bioSkills collection of 425 bioinformatics skills in one step, or only chosen categories, so sequencing, RNA-seq, single-cell and variant tasks get specialized help.
GPTomics/bioSkills
Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO.
GPTomics/bioSkills
Soft- or hard-clips PCR primer footprints from aligned amplicon BAMs so primer bases stop masquerading as confirmed reference sequence.
GPTomics/bioSkills
Filters BAM alignments by FLAG bits, mapping quality and regions with samtools view or pysam, with recipes for common keep and drop cases.
GPTomics/bioSkills
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam.
Categories
Map translation initiation sites, including non-AUG and alternative starts, from initiation-drug ribosome profiling (TI-seq). Bio Ribo Seq Initiation Site Mapping is an agent skill from GPTomics/bioSkills. Map translation initiation sites, including non-AUG and alternative starts, from initiation-drug ribosome profiling (TI-seq).
Bio Ribo Seq Initiation Site Mapping fits situations like: locating start codons; detecting near-cognate; upstream initiation; analyzing harringtonine.
Run `npx skills add GPTomics/bioSkills --skill bio-ribo-seq-initiation-site-mapping -a claude-code`. Or copy the skill folder (ribo-seq/initiation-site-mapping in GPTomics/bioSkills) into .claude/skills/bio-ribo-seq-initiation-site-mapping in your project. Claude Code loads it when a task matches its description.
Run `npx skills add GPTomics/bioSkills --skill bio-ribo-seq-initiation-site-mapping -a codex`. Or copy the skill folder (ribo-seq/initiation-site-mapping in GPTomics/bioSkills) into .agents/skills/bio-ribo-seq-initiation-site-mapping in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add GPTomics/bioSkills --skill bio-ribo-seq-initiation-site-mapping -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-ribo-seq-initiation-site-mapping, .gemini/skills/bio-ribo-seq-initiation-site-mapping, .github/skills/bio-ribo-seq-initiation-site-mapping and .opencode/skills/bio-ribo-seq-initiation-site-mapping in your project.
Going by SKILL.md and its folder, Bio Ribo Seq Initiation Site Mapping needs a shell for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: A Bash shell.
SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
Bio Ribo Seq Initiation Site Mapping is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 2k tokens (SKILL.md is roughly 8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
Skills that share tags, products or a category with Bio Ribo Seq Initiation Site Mapping: Translation Diff Export (Devolutions/UniGetUI, 26k stars), Sync Translations (symfony/symfony, 31k stars), Translation Diff Import (Devolutions/UniGetUI, 26k stars) and Translation Diff Translate (Devolutions/UniGetUI, 26k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
GPTomics (a GitHub organization) maintains it in GPTomics/bioSkills, which has 1,217 GitHub stars. The repository holds 559 skills in this directory. The repository was last updated on August 15, 2026.
Source: GPTomics/bioSkills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.