Research, academic papers, education, and exam prep (4.4K skills)
Find candidate guide RNAs for CRISPR experiments by scanning target DNA sequences. Rank candidates using sequence features and predicted activity, optionally restrict them to coding regions, and identify guides for Cas12a.
Design donor DNA templates for precise CRISPR insertions or sequence replacement. Choose between single-stranded DNA, double-stranded DNA, and plasmid donors, then construct matching flanking sequences and primers for amplification or assembly.
Design guide RNA sequences for prime editing, a method for precise DNA changes. Generate components for substitutions, small insertions, and deletions, compare primer binding lengths, and assemble complete sequences for experimental planning.
Design guide sequences for C-to-T or A-to-G base editing by comparing target positions, nearby bases that may also change, and sequence context. Includes Python examples for ranking candidates and considering paired edits.
Build evolutionary trees with a time axis from genetic sequences and sample dates using TreeTime. Estimate outbreak origins, mutation rates, ancestral sequences, and geographic spread, with guidance for BEAST2 analyses that include uncertainty estimates.
Search scientific papers through the BGPT MCP server and retrieve structured experimental details extracted from full texts. Gather methods, numerical results, sample sizes, quality assessments, and conclusions to compare studies and build evidence tables.
Search arXiv preprints, research papers shared before peer review, using everyday language. Find work across physics, mathematics, computer science, and quantitative biology, with article text and figure links returned through Valyu’s meaning-based search.
Predict structures for designed protein sequences and protein complexes with AlphaFold2 or ColabFold. Inspect structure files and confidence scores to assess folding and chain interfaces, with guidance for local runs, Modal execution, and common prediction errors.
Choose tools for designing proteins that bind a target. Compare BoltzGen, BindCraft, RFdiffusion, and Germinal by target type, design diversity, and validation needs, then plan target preparation, design generation, and candidate filtering.
Plan and troubleshoot molecular binding experiments using SPR and BLI, two optical measurement methods. Compare platforms, investigate weak signals or unwanted binding, adjust experimental conditions, and assess the quality of binding-rate measurements.
Search BindingDB for measured interactions between compounds and protein targets. Compare binding measurements, examine which targets a compound binds to, and prepare datasets for drug discovery research or machine learning using target identifiers, compound names, or chemical structures.
Look up genetic variants in ClinVar to retrieve pathogenicity classifications, review status, and associated diseases. Search by variant ID, gene, or HGVS notation, a standard variant description, or annotate local variant files in batches.
Identify super-enhancers, large clusters of gene regulatory regions, from H3K27ac ChIP-seq data. Use ROSE to join nearby peaks and rank their signals, then associate regions with nearby genes or compare experimental conditions.
Plan A/B experiments to measure the effect of a design change. Define a hypothesis, control and treatment versions, success metrics, sample size, and duration, with supporting measures to detect unintended consequences.
Turn a single user interview transcript into a structured summary with key themes, supporting quotes, pain points, and follow-up actions. Distinguish explicit statements from inferred insights to help stakeholders assess the findings.
Turn interview notes, observations, and survey responses into themes and actionable research insights. Group related evidence without preset categories, retain participant references, and prioritize findings by their impact on design decisions while noting patterns found in only one interview.
Design surveys to measure user opinions, needs, and satisfaction across a population. Plan neutral questions, clear response scales, participant sampling, and analysis methods to quantify findings and support decisions.
Design a shared research library that connects individual findings to studies and source data. Define tags, confidence levels, and maintenance routines so teams can find existing evidence, reuse past work, and track findings that become outdated.
Prepare a user interview guide with opening remarks, background questions, deeper exploration, and a closing section. It includes neutral questions, follow-up prompts, and facilitator notes to help uncover real experiences, behaviors, and motivations.
Create a diary study plan to understand user behavior over days or weeks. Define participant criteria, recording prompts, timing, capture methods, check-ins, and analysis, including ways to keep participants engaged throughout the study.
Turn user research into an empathy map covering what one user or segment says, thinks, does, and feels. Summarize goals, frustrations, design implications, and unanswered questions to help teams share an understanding of their users.
Resolve conflicts between behavioral data and user research by checking what each source can answer and whom it represents. Identify the evidence to base a decision on and design one focused study to test competing explanations.
Investigate a defined question using web sources, data experiments, or both. Keep evidence and experiment records together, then produce a structured verdict with caveats, including an inconclusive result when the available evidence does not settle the question.
Explore a topic by dividing it into three to five subtopics, explaining factual findings, and bringing them together in a structured summary that highlights uncertainty, open questions, and useful directions for further research.