R08.08.01.01 · 任务小类

通路与网络建模

Pathway & network modeling

Build, simulate and lay out biological networks.

20 条本项目编写的提案 · 分类 v1.1 · 新增基准运行 0 次。下方验证方式与部分得分规则是设计，不是执行结果。

典型应用: Cytoscape · COPASI · CellDesigner
小类 GUI 需求标签: HY · 混合

任务提案 · 20

展开查看完整原文与建议检查方式；两种界面均保留提案英文原文。

R08.08.01.01-T01 Import an interaction table into Cytoscape and style it by a layout and attributes

原始指令

In Cytoscape import input/interactions.tsv (source, target, score) as a network and input/node_attrs.csv as a node table. Apply the prefuse force-directed layout weighted by score, map node fill colour to log2FC (blue–white–red, −3 to 3), node size to degree (20–60), and edge transparency to score. Save output/network.cys and export output/network.png at 300 dpi.

平台: mac · macOS win · Windows lin · Linux
应用: Cytoscape
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: AP · API 足够
交互原语: click · 指向与点击 drag · 拖放 type · 文字与表单
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 2 / 5

建议验证方式

Session parsed: node/edge counts equal the input; visual style mappings exactly as stated (continuous mappings with the given ranges); layout weighted by score (node positions correlate with the reference layout's edge-length distribution); PNG 300 dpi.

建议部分得分

25% network imported with attributes; 40% style mappings; 20% layout; 15% export.

R08.08.01.01-T02 Find and annotate dense modules with MCODE in Cytoscape

原始指令

In Cytoscape open input/ppi.cys and run clusterMaker2's MCODE (degree cutoff 2, node score cutoff 0.2, k-core 2) on the whole network. Keep clusters with ≥6 nodes, create a subnetwork per cluster, name them Cluster_1..n by score, and export output/clusters.csv (node, cluster) plus output/cluster_scores.csv.

平台: mac · macOS win · Windows lin · Linux
应用: Cytoscape · clusterMaker2
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: AP · API 足够
交互原语: click · 指向与点击 type · 文字与表单
工作产物: WP02 · 记录 / 表格
条件: 未声明
提案难度: 3 / 5

建议验证方式

Cluster membership must match the reference MCODE run at those parameters (ARI ≥0.95); subnetwork count and naming by descending score correct; scores within 0.01.

建议部分得分

40% membership; 25% size filter; 20% subnetworks named; 15% exports.

R08.08.01.01-T03 Build a three-species Lotka–Volterra model in COPASI and report the steady state

原始指令

In COPASI build the reactions in input/model_spec.pdf (one resource, two consumers) with mass-action kinetics and the given rate constants and initial concentrations. Run a time course to t=500 (step 0.1), then Steady State analysis, and save output/model.cps plus output/steady_state.csv with concentrations and the Jacobian eigenvalues.

平台: win · Windows mac · macOS lin · Linux
应用: COPASI
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单
工作产物: WP07 · 仿真结果
条件: 未声明
提案难度: 3 / 5

建议验证方式

SBML export of model.cps must match the gold reaction network and parameters; steady-state concentrations within 1e-4 relative error and eigenvalue real parts matching the reference stability classification.

建议部分得分

35% model structure and parameters; 25% time course runs; 30% steady state; 10% exports.

R08.08.01.01-T04 Reproduce bistability by scanning a parameter in COPASI

原始指令

Open input/toggle_switch.cps in COPASI. Run two steady-state parameter scans of k_ind over 0–2 in 200 steps, one upward started from the low-expression state and one downward from the high state, locate the hysteresis (bistable) range, and write output/scan.csv plus output/answer.json with the two bifurcation values. Save output/scanned.cps.

平台: win · Windows mac · macOS lin · Linux
应用: COPASI
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物: WP07 · 仿真结果
条件: 未声明
提案难度: 4 / 5

建议验证方式

Bifurcation values within 2% of reference; scan.csv must contain both sweeps (2×201 rows) with steady-state values consistent with the task settings (scan task saved in the .cps).

建议部分得分

30% scan configured; 25% scan output; 45% bifurcation values.

R08.08.01.01-T05 Fit model parameters to time-course data in COPASI and report the fit

原始指令

Open input/mm_model.cps and import input/timecourse.csv as experimental data in COPASI's Parameter Estimation. Estimate Vmax and Km with the Levenberg–Marquardt method (bounds in input/bounds.txt), and write output/fit.json (parameter values, objective value, RSS) and save output/fitted.cps.

平台: win · Windows mac · macOS lin · Linux
应用: COPASI
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物: WP07 · 仿真结果
条件: 未声明
提案难度: 3 / 5

建议验证方式

Estimated Vmax and Km within 5% of the reference fit and RSS within 5%; data mapping must assign the right experimental columns to species (mismapping changes RSS by >50%).

建议部分得分

30% data mapped; 25% estimation configured; 35% parameter values; 10% RSS reported.

R08.08.01.01-T06 Draw an SBGN-compliant MAPK cascade in CellDesigner and export SBML

原始指令

In CellDesigner draw the three-tier MAPK cascade described in input/cascade.pdf with correct SBGN species types (generic protein, phosphorylated residues as modification sites), catalysis arcs for each kinase, and a phosphatase for each tier. Lay it out top to bottom and save output/mapk.xml (SBML Level 2) plus output/mapk.png.

平台: mac · macOS win · Windows lin · Linux
应用: CellDesigner
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 drag · 拖放 type · 文字与表单
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 4 / 5

建议验证方式

SBML parsed: species count and modification states equal gold; every phosphorylation reaction has the correct catalyst modifier and each tier a phosphatase; layout y-coordinates ordered by tier (MAP3K above MAP2K above MAPK). CellDesigner plugins are disabled, python-libsbml is absent, and a file-system audit flags files not written by CellDesigner.

建议部分得分

30% species and modifications; 30% catalysis arcs; 20% phosphatases; 20% layout order.

R08.08.01.01-T07 Compute network statistics in Cytoscape and report the top hub proteins

原始指令

In Cytoscape open input/ppi.cys and run NetworkAnalyzer on the undirected network. Report the five nodes with highest degree and the five with highest betweenness in output/answer.json, and export the full node statistics table to output/node_stats.csv.

平台: mac · macOS win · Windows lin · Linux
应用: Cytoscape
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: AP · API 足够
交互原语: click · 指向与点击 nav · 平移 / 缩放 / 滚动
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 2 / 5

建议验证方式

Both top-five lists must equal gold in order (ties resolved by node name); betweenness values within 1% of the reference computation on the same network (self-loops excluded).

建议部分得分

40% degree top-five; 40% betweenness top-five; 20% statistics export.

R08.08.01.01-T08 Overlay expression data on a KEGG pathway in Cytoscape and style a legend

原始指令

In Cytoscape import the KEGG pathway in input/hsa04151.xml with the KEGGscape importer, load input/expression.csv onto nodes, map fill colour to log2FC (−2 to 2 diverging) and node border width to −log10(padj), hide unmeasured nodes' colour mapping to grey, add a legend, and save output/pathway.cys and output/pathway.pdf.

平台: mac · macOS win · Windows lin · Linux
应用: Cytoscape
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: AP · API 足够
交互原语: click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 3 / 5

建议验证方式

Node mapping checked for 20 sampled genes (colour within ±10 RGB of the mapping, border widths proportional); unmeasured nodes grey; legend present in the PDF (text extraction); pathway topology equals the KGML.

建议部分得分

25% pathway import; 35% colour mapping; 20% border mapping and grey default; 20% legend and export.

R08.08.01.01-T09 Run stochastic and deterministic simulations of a gene-expression model in COPASI

原始指令

Open input/gene_expr.cps in COPASI. Run a deterministic (LSODA) time course to t=1000 and 50 stochastic (Gibson–Bruck) runs with the same duration, export both to output/det.csv and output/stoch.csv, and write mean and CV of protein at t=1000 across stochastic runs in output/answer.json.

平台: win · Windows mac · macOS lin · Linux
应用: COPASI
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单
工作产物: WP07 · 仿真结果
条件: 未声明
提案难度: 3 / 5

建议验证方式

Deterministic trajectory within 1e-3 relative error of reference; stochastic mean within 5% of the deterministic value and CV within 15% of the reference ensemble; 50 runs present in the export.

建议部分得分

30% deterministic run; 30% 50 stochastic runs; 30% mean and CV; 10% exports.

R08.08.01.01-T10 Merge two interaction networks in Cytoscape and resolve identifier conflicts

原始指令

In Cytoscape import input/net_symbols.tsv (gene symbols) and input/net_uniprot.tsv (UniProt accessions), map both to Entrez IDs using input/id_map.csv, merge with union keeping provenance per edge, remove duplicate and self edges, and save output/merged.cys plus output/merged_edges.csv.

平台: mac · macOS win · Windows lin · Linux
应用: Cytoscape
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: AP · API 足够
交互原语: click · 指向与点击 type · 文字与表单
工作产物: WP02 · 记录 / 表格
条件: hidden · 隐藏 / 过期状态
提案难度: 4 / 5

建议验证方式

Merged node and edge sets equal gold (after ID normalization); each edge carries a source-network provenance attribute; zero self-loops and duplicate edges; ambiguous IDs in id_map.csv handled as gold specifies (one-to-many dropped).

建议部分得分

30% ID mapping; 35% merged edge set; 20% provenance; 15% cleanup.

R08.08.01.01-T11 Build a Boolean regulatory network in GINsim and compute its attractors

原始指令

In GINsim build the Boolean model in input/boolean_spec.txt (6 nodes with the given logical rules), run stable-state and attractor search over the full state space, and export the model to output/model.zginml and the attractor list to output/attractors.csv.

平台: mac · macOS win · Windows lin · Linux
应用: GINsim
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 drag · 拖放 type · 文字与表单
工作产物: WP07 · 仿真结果
条件: tutorial · 阅读文档 / 教程
提案难度: 4 / 5

建议验证方式

Logical rules in the exported model equal gold (truth tables per node); attractor set (stable states and cyclic attractors) equals the reference computation exactly. bioLQM is absent and GINsim's -s script mode is disabled; the .zginml must hold GINsim's rule objects.

建议部分得分

40% logical rules; 40% attractors; 20% exports valid.

R08.08.01.01-T12 Control: build and solve the three-species model with Tellurium

原始指令

Control pair of T03. Without a GUI, encode the reactions in input/model_spec.pdf (mass action, given constants and initial concentrations) in Antimony with Tellurium, simulate to t=500 (step 0.1), compute the steady state and Jacobian eigenvalues, and write output/model.xml (SBML) and output/steady_state.csv.

平台: lin · Linux mac · macOS
应用: Tellurium · libRoadRunner
交互表面: term · 终端
GUI 需求 · 任务设定: CL · CLI 足够
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令
工作产物: WP07 · 仿真结果
条件: 未声明
提案难度: 2 / 5

建议验证方式

Same checker as T03: SBML network and parameters equal gold, steady-state concentrations within 1e-4 relative error, eigenvalue real parts give the reference stability class. Scored as the CLI control of T03.

建议部分得分

35% model structure; 25% simulation; 30% steady state; 10% outputs.

R08.08.01.01-T13 Visualize a flux distribution on an Escher map and export it

原始指令

In Escher (web) load the E. coli core map and the reaction data in input/fluxes.json, then in Settings style reactions by colour and size using absolute values, scale grey (0) to red (max) and width 2–20 px. Export output/map.svg and a 1600×1200 output/map.png, and report the three highest-flux reactions in output/answer.json.

平台: web · 任意系统（网页）
应用: Escher
交互表面: brow · 浏览器
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 drag · 拖放 vis · 视觉判断
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 3 / 5

建议验证方式

SVG parsed: for 20 sampled reactions, path stroke colour (±15 RGB) and width (±1 px) follow the stated scale for |flux|; top three reactions equal gold; PNG size correct. The cobrapy/escher Python packages are absent, so styling must come from the Escher settings panel, and a file-system audit flags exports not saved by the browser.

建议部分得分

30% data loaded; 40% colour and width scale; 20% top reactions; 10% exports.

R08.08.01.01-T14 Lay out a 400-node network for publication with manual module placement

原始指令

In Cytoscape open input/large_net.cys (400 nodes, 9 annotated modules). Produce a readable figure: place each module as a visually separated group (yEd-style or manual drag after per-group layout), avoid edge crossings between neighbouring modules, label each group, and export output/figure.pdf plus output/layout.cys.

平台: mac · macOS win · Windows lin · Linux
应用: Cytoscape
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: drag · 拖放 click · 指向与点击 vis · 视觉判断 nav · 平移 / 缩放 / 滚动
工作产物: WP03 · 视觉排版
条件: long · 长流程
提案难度: 4 / 5

建议验证方式

From saved coordinates: within-module mean pairwise distance < 0.4× between-module centroid distance for all 9 modules; no node overlaps; 9 group labels present; inter-module edge crossings below the reference automatic-layout count. Automatic layouts alone cannot meet the separation bound (reference layout check). CyREST and the Command Line Dialog are disabled and py4cytoscape is absent.

建议部分得分

40% module separation; 20% no overlaps; 20% crossing count; 20% labels and export.

R08.08.01.01-T15 Fix an SBML model that fails validation and reproduce a published figure

原始指令

input/broken_model.xml fails SBML validation (unit errors, a missing initial assignment and an unbalanced reaction). Fix it in COPASI, run the time course in input/figure_spec.txt and compare with the digitized reference input/figure_data.csv. Save output/fixed.xml, output/sim.csv and output/notes.md listing each fix.

平台: win · Windows mac · macOS lin · Linux
应用: COPASI
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物: WP07 · 仿真结果
条件: long · 长流程
提案难度: 5 / 5

建议验证方式

libSBML validation reports zero errors; simulated trajectory within 5% RMSE of figure_data.csv; notes.md must name all three seeded defects.

建议部分得分

35% validation clean; 40% trajectory match; 25% fixes documented.

R08.08.01.01-T16 Build a rule-based signalling model in BioNetGen and compare with a reduced ODE model

原始指令

Write output/model.bngl implementing the receptor–ligand–adaptor rules in input/rules_spec.md with the given rate constants, simulate with NFsim to t=600, then build the reduced ODE model in COPASI from input/reduced_spec.txt and simulate the same window. Save output/bng.gdat, output/ode.csv and output/compare.md explaining where they diverge.

平台: lin · Linux mac · macOS
应用: BioNetGen · COPASI
交互表面: term · 终端 desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令 click · 指向与点击 vis · 视觉判断
工作产物: WP07 · 仿真结果
条件: long · 长流程 multiapp · 多应用
提案难度: 5 / 5

建议验证方式

BNGL species and observables match gold (species graph check); NFsim trajectory within 8% of reference at 10 sampled times; ODE run matches its reference; compare.md must identify the divergence caused by the neglected dimer state (keyword check).

建议部分得分

30% rule model correct; 25% stochastic simulation; 25% ODE simulation; 20% divergence analysis.

R08.08.01.01-T17 Run network enrichment in Cytoscape with stringApp and build an enrichment figure

原始指令

In Cytoscape use stringApp to retrieve the STRING network for the 85 genes in input/genes.txt (human, confidence ≥0.7), run functional enrichment, keep GO Biological Process terms with FDR <0.01, colour nodes by the top three terms as a split donut style, and save output/string.cys plus output/enrichment.csv.

平台: mac · macOS win · Windows lin · Linux
应用: Cytoscape · stringApp
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 3 / 5

建议验证方式

The grader reruns the identical stringApp query at grading time: node count within 5% and enrichment terms and FDRs matching that rerun; the three top terms are mapped as node charts in the saved style.

建议部分得分

30% network retrieval; 30% enrichment table; 25% chart styling; 15% session saved.

R08.08.01.01-T18 Make a COPASI model match an experiment by choosing which parameters to fit

原始指令

input/model_v1.cps underfits input/data.csv (RSS 48). Decide which three of the eight parameters to estimate (the others are measured and fixed per input/measured.txt), run parameter estimation, and reach RSS <6 without any parameter leaving its physical bounds. Save output/model_v2.cps and output/choice.md justifying the selection.

平台: win · Windows mac · macOS lin · Linux
应用: COPASI
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物: WP07 · 仿真结果
条件: long · 长流程
提案难度: 5 / 5

建议验证方式

RSS <6 on the given data and <12 on a hidden replicate (guards overfitting); measured parameters unchanged; all estimated values within bounds; choice.md names the three parameters that the reference sensitivity analysis identifies.

建议部分得分

25% parameter choice; 35% RSS on fit data; 25% hidden replicate; 15% constraints respected.

R08.08.01.01-T19 Annotate a CellDesigner pathway with database identifiers and validate SBML

原始指令

Open input/pathway.xml in CellDesigner and add MIRIAM annotations to all 24 species (UniProt for proteins, ChEBI for metabolites) using the identifiers in input/ids.csv, plus a model-level publication annotation. Save output/annotated.xml and verify with the SBML validator that there are no errors.

平台: mac · macOS win · Windows lin · Linux
应用: CellDesigner
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 3 / 5

建议验证方式

All 24 species carry a bqbiol:is annotation with the correct resource URI from ids.csv; model has a bqmodel:isDescribedBy entry; libSBML validation reports zero errors; diagram layout unchanged. python-libsbml is not installed and a file-system audit log flags an annotated.xml not written by CellDesigner, whose layout must stay intact.

建议部分得分

60% species annotations (scaled); 20% model annotation; 20% validation clean.

R08.08.01.01-T20 Compare two clustering algorithms on the same network and justify the better one

原始指令

In Cytoscape open input/ppi.cys and run clusterMaker2 MCL (inflation 2.5) and community detection (Leiden, resolution 1.0). Export both memberships to output/mcl.csv and output/leiden.csv, compare them against the reference complexes in input/complexes.csv, and recommend one in output/recommendation.md with the matching statistic you used.

平台: mac · macOS win · Windows lin · Linux
应用: Cytoscape · clusterMaker2
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 3 / 5

建议验证方式

Both memberships match reference runs (ARI ≥0.95 each); the recommendation must name the algorithm with the higher F-measure against complexes.csv (computed by the grader, margin >0.03), and the reported statistic must be within 0.02 of the grader's value.

建议部分得分

35% both clusterings; 25% comparison statistic; 30% correct recommendation; 10% exports.

已有研究映射

当前映射未给此小类指定基准参考。