@datagrok/bio 2.27.8 → 2.27.9

package/files/demo-files/bio_similarity_diversity.layout

@@ -0,0 +1,205 @@
+{
+  "#type": "ViewLayout",
+  "viewStateMap": {
+    "containerType": "horizontal",
+    "state": {
+      "width": 1616,
+      "height": 833
+    },
+    "children": [
+      {
+        "containerType": "fill",
+        "state": {
+          "width": 812,
+          "height": 833,
+          "documentManager": true
+        },
+        "children": [
+          {
+            "containerType": "panel",
+            "state": {
+              "width": 812,
+              "height": 833,
+              "element": {
+                "id": "4a541150-48b0-11f1-921a-4b0415f08584",
+                "type": "Grid",
+                "look": {
+                  "#type": "GridLook",
+                  "showAddNewRowIcon": true,
+                  "addNewRowOnLastRowEdit": true,
+                  "rowHeight": 30,
+                  "topLevelDefaultMenu": true,
+                  "allowColumnMenu": true,
+                  "columns": [
+                    {
+                      "width": 44,
+                      "backgroundColor": 4294440951,
+                      "customName": "",
+                      "cellType": "row header",
+                      "headerCellStyle": {
+                        "textWrap": "words"
+                      }
+                    },
+                    {
+                      "width": 230,
+                      "columnName": "sequence",
+                      "cellType": "sequence",
+                      "headerCellStyle": {
+                        "textWrap": "words"
+                      }
+                    },
+                    {
+                      "width": 155,
+                      "columnName": "Activity",
+                      "customFormat": "0.0000000000000000",
+                      "cellType": "number",
+                      "format": "0.0000000000000000",
+                      "headerCellStyle": {
+                        "textWrap": "words"
+                      }
+                    }
+                  ],
+                  "onInitializedScript": "\n      setTimeout(async () => {\n        const t = grok.shell.table('Table');\n        if (!t)\n          return;\n        await t.meta.detectSemanticTypes();\n        const func = DG.Func.find({name: 'hierarchicalClustering'})[0];\n        if (!func)\n          return;\n        const cols = [\"sequence\"];\n        func.apply({\n          df: t,\n          colNameList: cols,\n          distance: 'euclidean',\n          linkage: 'complete'\n        });\n      }, 1000)\n    "
+                },
+                "title": "peptides-non-natural",
+                "default": true
+              }
+            },
+            "children": []
+          }
+        ]
+      },
+      {
+        "containerType": "vertical",
+        "state": {
+          "width": 803,
+          "height": 833
+        },
+        "children": [
+          {
+            "containerType": "panel",
+            "state": {
+              "width": 803,
+              "height": 396,
+              "element": {
+                "id": "4a543860-48b0-11f1-83c0-f546b6d79614",
+                "type": "Sequence Similarity Search",
+                "look": {
+                  "#type": "JsViewerHostLook",
+                  "limit": 10,
+                  "targetColumnName": "sequence",
+                  "distanceMetric": "Hamming",
+                  "fingerprint": "Morgan",
+                  "gapOpen": 1,
+                  "gapExtend": 0.6,
+                  "cutoff": 0.01,
+                  "hotSearch": true,
+                  "similarColumnLabel": null
+                },
+                "title": "Sequence Similarity Search"
+              }
+            },
+            "children": []
+          },
+          {
+            "containerType": "panel",
+            "state": {
+              "width": 803,
+              "height": 436,
+              "element": {
+                "id": "4a545f70-48b0-11f1-8ba2-6d41f5aaac0d",
+                "type": "Sequence Diversity Search",
+                "look": {
+                  "#type": "JsViewerHostLook",
+                  "limit": 10,
+                  "targetColumnName": "sequence",
+                  "distanceMetric": "Hamming",
+                  "fingerprint": "Morgan",
+                  "gapOpen": 1,
+                  "gapExtend": 0.6,
+                  "diverseColumnLabel": null
+                },
+                "title": "Sequence Diversity Search"
+              }
+            },
+            "children": []
+          }
+        ]
+      }
+    ],
+    "floating": [],
+    "tableId": "1ac6c220-48b0-11f1-96f8-25bc74a4f3be",
+    "tableName": "Table"
+  },
+  "userData": {
+    ".columnTags": {
+      "sequence": {
+        "units": "separator",
+        "cell.renderer": "sequence",
+        "quality": "Macromolecule"
+      },
+      "Activity": {
+        "format": "0.0000000000000000"
+      }
+    }
+  },
+  "columns": [
+    {
+      "name": "sequence",
+      "type": "string",
+      "semType": "Macromolecule",
+      "id": "4a5522c0-48b0-11f1-aa6b-0144c5d96cd0",
+      "friendlyName": "Sequence",
+      "entityTags": [
+        {
+          "tag": "units",
+          "id": "4a54ad90-48b0-11f1-b76c-7b84e409c4c8"
+        },
+        {
+          "tag": "separator",
+          "id": "4a54ad90-48b0-11f1-a63d-e750540d4500"
+        },
+        {
+          "tag": "aligned",
+          "id": "4a54ad90-48b0-11f1-bacb-b7efc320ed4f"
+        },
+        {
+          "tag": "alphabet",
+          "id": "4a54d4a0-48b0-11f1-e38d-791eed2bbb06"
+        },
+        {
+          "tag": ".alphabetIsMultichar",
+          "id": "4a54d4a0-48b0-11f1-d005-9b6dd0639b69"
+        },
+        {
+          "tag": "cell.renderer",
+          "id": "4a54fbb0-48b0-11f1-f185-1736b856a5fd"
+        },
+        {
+          "tag": "quality",
+          "id": "4a54fbb0-48b0-11f1-9edd-8bfb44ec952c"
+        },
+        {
+          "tag": ".semantic-detection-duration",
+          "id": "4a54fbb0-48b0-11f1-a122-c1e30be38aa5"
+        }
+      ],
+      "metaParams": {
+        "units": "separator",
+        "separator": "/",
+        "aligned": "SEQ.MSA",
+        "alphabet": "UN",
+        ".alphabetIsMultichar": "true",
+        "cell.renderer": "sequence",
+        "quality": "Macromolecule",
+        ".semantic-detection-duration": "17"
+      }
+    }
+  ],
+  "name": "Table",
+  "friendlyName": "Table",
+  "author": {
+    "id": "cb276bc0-6280-11ee-82f7-8dc8dd5df45b"
+  },
+  "createdOn": "2026-05-10T15:59:56.643Z"
+}

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.27.8",
+  "version": "2.27.9",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",

package/src/demo/bio01-similarity-diversity.ts

@@ -30,6 +30,16 @@ export async function demoBioSimDiv() {
     {df: grok.shell.t, colNameList: ['sequence'], distance: 'euclidian', linkage: 'complete'});
 }
 
+export async function demoBioSimDivLayout() {
+  const t = await _package.files.readCsv('samples/peptides-non-natural.csv');
+  const tv = grok.shell.addTableView(t);
+  _package.files.readAsText('demo-files/bio_similarity_diversity.layout').then(async (layoutString: string) => {
+    const layout = DG.ViewLayout.fromJson(layoutString);
+    await DG.delay(100);
+    tv.loadLayout(layout);
+  });
+}
+
 export async function demoBio01UISteps() {
   const seqHelper: ISeqHelper = await getSeqHelper();
 

package/src/demo/bio01a-hierarchical-clustering-and-sequence-space.ts

@@ -16,7 +16,6 @@ export async function demoSeqSpace() {
   const p = await grok.functions.eval('Bio:SeqSpaceDemo');
   const project = await grok.dapi.projects.find(p.id);
   await project.open();
-  grok.shell.windows.help.showHelp('/help/datagrok/solutions/domains/bio/bio.md#sequence-space');
 }
 
 export async function demoBio01aUI() {

package/src/demo/bio01b-hierarchical-clustering-and-activity-cliffs.ts

@@ -157,3 +157,28 @@ export async function demoActivityCliffsCyclic() {
   }
   grok.shell.windows.help.showHelp('/help/datagrok/solutions/domains/bio/bio.md#activity-cliffs');
 }
+
+
+export async function demoActivityCliffsCyclicLayout(): Promise<void> {
+  grok.shell.windows.showContextPanel = true;
+  const p = await grok.functions.eval('Bio:BioDemoActivityCliffs');
+  const project = await grok.dapi.projects.find(p.id);
+  await project.open();
+  let scatterPlot: DG.Viewer | null = null;
+  for (const i of grok.shell.tv.viewers) {
+    if (i.type == DG.VIEWER.SCATTER_PLOT)
+      scatterPlot = i;
+  }
+  let cliffsLink;
+  try {
+    await awaitCheck(() => {
+      const link = scatterPlot?.root.getElementsByClassName('scatter_plot_link');
+      if (link?.length) {
+        cliffsLink = link[0];
+        return true;
+      }
+      return false;
+    }, '', 10000);
+    (cliffsLink as any as HTMLElement).click();
+  } catch (e) {}
+}

package/src/demo/bio03-atomic-level.ts

@@ -6,20 +6,6 @@ import {handleError} from './utils';
 import {DemoScript} from '@datagrok-libraries/tutorials/src/demo-script';
 import {adjustGridcolAfterRender} from '../utils/ui-utils';
 
-export async function demoToAtomicLevel(): Promise<void> {
-  const data = await _package.files.readCsv('samples/HELM_BI_CYCLIC.csv');
-  data.name = 'To Atomic Level';
-  await data.meta.detectSemanticTypes();
-  await grok.data.detectSemanticTypes(data);
-  const view = grok.shell.addTableView(data);
-  const seqCol = data.col('HELM')!;
-  await PackageFunctions.toAtomicLevel(data, seqCol, true, false);
-  adjustGridcolAfterRender(view.grid, 'molfile(HELM)', 500, 300, true);
-  adjustGridcolAfterRender(view.grid, 'HELM', 500, undefined, true);
-  grok.shell.info('Hover over monomers in HELM column to highlight them in molecular structure.', {timeout: 10});
-  grok.shell.windows.help.showHelp('/help/datagrok/solutions/domains/bio/bio.md#convert-to-atomic-level');
-}
-
 export async function demoBio03UI(): Promise<void> {
   const dataFn: string = 'samples/HELM.csv';
   const seqColName = 'HELM';

package/src/demo/feature_demos.ts

@@ -0,0 +1,103 @@
+/* eslint-disable max-len */
+import * as DG from 'datagrok-api/dg';
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import {_package} from '../package';
+import {adjustGridcolAfterRender} from '../utils/ui-utils';
+import {buildMonomerHoverLink} from '@datagrok-libraries/bio/src/monomer-works/monomer-hover';
+import {ChemTags} from '@datagrok-libraries/chem-meta/src/consts';
+
+export async function antibodyDemo() {
+  // for some reason the col is not saved in the layout
+  const antibodyTags = [
+    [
+      'units',
+      'fasta'
+    ],
+    [
+      'aligned',
+      'SEQ.MSA'
+    ],
+    [
+      'alphabet',
+      'PT'
+    ],
+    [
+      'cell.renderer',
+      'sequence'
+    ],
+    [
+      'quality',
+      'Macromolecule'
+    ],
+    [
+      '.semantic-detection-duration',
+      '8'
+    ],
+    [
+      '.annotations',
+      '[{"id":"deamid-ng","name":"Deamidation (NG)","description":"deamidation liability pattern (111 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#E53935","severity":"high","motifPattern":"NG","autoGenerated":true},{"id":"deamid-ns","name":"Deamidation (NS)","description":"deamidation liability pattern (859 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#E53935","severity":"medium","motifPattern":"NS","autoGenerated":true},{"id":"deamid-na","name":"Deamidation (NA)","description":"deamidation liability pattern (69 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#E53935","severity":"low","motifPattern":"NA","autoGenerated":true},{"id":"deamid-nd","name":"Deamidation (ND)","description":"deamidation liability pattern (18 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#E53935","severity":"low","motifPattern":"ND","autoGenerated":true},{"id":"deamid-nt","name":"Deamidation (NT)","description":"deamidation liability pattern (546 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#E53935","severity":"low","motifPattern":"NT","autoGenerated":true},{"id":"isom-dg","name":"Isomerization (DG)","description":"isomerization liability pattern (118 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#FF9800","severity":"high","motifPattern":"DG","autoGenerated":true},{"id":"isom-ds","name":"Isomerization (DS)","description":"isomerization liability pattern (306 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#FF9800","severity":"medium","motifPattern":"DS","autoGenerated":true},{"id":"oxid-m","name":"Oxidation (Met)","description":"oxidation liability pattern (1220 hits)","start":null,"end":null,"visualType":"point","category":"liability","color":"#9C27B0","severity":"medium","motifPattern":"M","autoGenerated":true},{"id":"oxid-w","name":"Oxidation (Trp)","description":"oxidation liability pattern (2593 hits)","start":null,"end":null,"visualType":"point","category":"liability","color":"#9C27B0","severity":"low","motifPattern":"W","autoGenerated":true},{"id":"glyco-nxst","name":"N-glycosylation","description":"glycosylation liability pattern (38 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#4CAF50","severity":"high","motifPattern":"N[^P][ST]","autoGenerated":true},{"id":"free-cys","name":"Free Cysteine","description":"freeCysteine liability pattern (2327 hits)","start":null,"end":null,"visualType":"point","category":"liability","color":"#607D8B","severity":"info","motifPattern":"C","autoGenerated":true},{"id":"kabat-heavy-fr1","name":"FR1","description":"FR1 (KABAT 1-30)","start":"1","end":"30","visualType":"region","category":"structure","sourceScheme":"KABAT","autoGenerated":true},{"id":"kabat-heavy-cdr1","name":"CDR1","description":"CDR1 (KABAT 31-35)","start":"31","end":"35","visualType":"region","category":"structure","sourceScheme":"KABAT","autoGenerated":true},{"id":"kabat-heavy-fr2","name":"FR2","description":"FR2 (KABAT 36-49)","start":"36","end":"49","visualType":"region","category":"structure","sourceScheme":"KABAT","autoGenerated":true},{"id":"kabat-heavy-cdr2","name":"CDR2","description":"CDR2 (KABAT 50-65)","start":"50","end":"65","visualType":"region","category":"structure","sourceScheme":"KABAT","autoGenerated":true},{"id":"kabat-heavy-fr3","name":"FR3","description":"FR3 (KABAT 66-94)","start":"66","end":"94","visualType":"region","category":"structure","sourceScheme":"KABAT","autoGenerated":true},{"id":"kabat-heavy-cdr3","name":"CDR3","description":"CDR3 (KABAT 95-102)","start":"95","end":"102","visualType":"region","category":"structure","sourceScheme":"KABAT","autoGenerated":true},{"id":"kabat-heavy-fr4","name":"FR4","description":"FR4 (KABAT 103-113)","start":"103","end":"113","visualType":"region","category":"structure","sourceScheme":"KABAT","autoGenerated":true}]'
+    ],
+    [
+      '.annotationColumnName',
+      '~AntibodyHC_annotations'
+    ],
+    [
+      '.id',
+      '750dcca0-48b0-11f1-e663-211b32f9e20c'
+    ],
+    [
+      '.numberingScheme',
+      'kabat'
+    ],
+    [
+      '.regions',
+      '[{"name":"FR1","description":"FR1 (KABAT 1-30)","start":"1","end":"30"},{"name":"CDR1","description":"CDR1 (KABAT 31-35)","start":"31","end":"35"},{"name":"FR2","description":"FR2 (KABAT 36-49)","start":"36","end":"49"},{"name":"CDR2","description":"CDR2 (KABAT 50-65)","start":"50","end":"65"},{"name":"FR3","description":"FR3 (KABAT 66-94)","start":"66","end":"94"},{"name":"CDR3","description":"CDR3 (KABAT 95-102)","start":"95","end":"102"},{"name":"FR4","description":"FR4 (KABAT 103-113)","start":"103","end":"113"}]'
+    ],
+    [
+      '.positionShift',
+      '42.10943057774151'
+    ]
+  ];
+  const df = await _package.files.readCsv('demo-files/Antibody_HC.csv');
+  const orCol = df.col('AntibodyHC')!;
+  antibodyTags.forEach(([k, v]) => orCol.setTag(k, v));
+  const clustCol = df.col('cluster (dbscan)')!;
+  const stCol = clustCol.convertTo(DG.TYPE.STRING);
+  df.columns.remove(clustCol.name);
+  df.columns.add(stCol);
+  const layoutTXT = await _package.files.readAsText('demo-files/Antibody_HC.layout');
+  const layout = DG.ViewLayout.fromJson(layoutTXT);
+  layout.columns.forEach((c) => {
+    const col = df.col(c.name);
+    if (col)
+      Object.entries(c.tags).forEach(([k, v]) => col.setTag(k, v));
+  });
+  const tv = grok.shell.addTableView(df);
+  await DG.delay(100);
+  tv.loadLayout(layout, true);
+}
+
+export async function atomicLevelDemo() {
+  const df = await _package.files.readCsv('demo-files/Atomic_Level.csv');
+  await df.meta.detectSemanticTypes();
+  const tv = grok.shell.addTableView(df);
+  await DG.delay(100);
+  await buildMonomerHoverLink(df.col('helm')!, df.col('molfile(helm)')!, _package.monomerLib, _package.seqHelper, _package.rdKitModule, true);
+  adjustGridcolAfterRender(tv.grid, 'molfile(HELM)', 500, 300, true);
+  adjustGridcolAfterRender(tv.grid, 'HELM', 500, undefined, true);
+  df.col('molfile(helm)')!.setTag(ChemTags.SEQUENCE_SRC_HL_MONOMERS, 'false');
+  df.col('molfile(helm)')!.setTag(ChemTags.SEQUENCE_SRC_COL, 'HELM');
+  grok.shell.info('Hover over monomers in HELM column to highlight them in molecular structure.', {timeout: 10});
+}
+
+export async function sirnaDemo() {
+  const df = await _package.files.readCsv('demo-files/SIRNA.csv');
+  const layoutTXT = await _package.files.readAsText('demo-files/SIRNA.layout');
+  const layout = DG.ViewLayout.fromJson(layoutTXT);
+  const tv = grok.shell.addTableView(df);
+  await DG.delay(100);
+  tv.loadLayout(layout, true);
+  await df.meta.detectSemanticTypes();
+  grok.shell.info('Hover over the oligo structrues to see modifications to different sugars, linkers and residues.', {timeout: 10});
+}

package/src/package-api.ts

@@ -498,10 +498,24 @@ export namespace funcs {
     return await grok.functions.call('Bio:DemoBioAtomicLevel', {});
   }
 
+  /**
+  SI-RNA sequences, molecular structures, curves and assay data
+  */
+  export async function demoBioSiRNA(): Promise<void> {
+    return await grok.functions.call('Bio:DemoBioSiRNA', {});
+  }
+
   export async function sdfToJsonLib(table: DG.DataFrame ): Promise<void> {
     return await grok.functions.call('Bio:SdfToJsonLib', { table });
   }
 
+  /**
+  Antibody sequences, numbering, liabilities, extraction and SAR
+  */
+  export async function demoAntibodies(): Promise<void> {
+    return await grok.functions.call('Bio:DemoAntibodies', {});
+  }
+
   /**
   Converts a `Macromolecule` sequence to its atomic level `Molecule` representation
   */

package/src/package.g.ts

@@ -753,18 +753,34 @@ export async function demoBioActivityCliffs() : Promise<void> {
 }
 
 //description: Atomic level structure of Macromolecules
+//meta.demoSkip: true
 //meta.demoPath: Bioinformatics | Atomic Level
 //meta.path: /apps/Tutorials/Demo/Bioinformatics/Atomic%20Level
 export async function demoBioAtomicLevel() : Promise<void> {
   await PackageFunctions.demoBioAtomicLevel();
 }
 
+//description: SI-RNA sequences, molecular structures, curves and assay data
+//meta.demoSkip: true
+//meta.demoPath: Bioinformatics | SI-RNA
+//meta.path: /apps/Tutorials/Demo/Bioinformatics/SI-RNA
+export async function demoBioSiRNA() : Promise<void> {
+  await PackageFunctions.demoBioSiRNA();
+}
+
 //name: SDF to JSON Library
 //input: dataframe table 
 export async function sdfToJsonLib(table: DG.DataFrame) : Promise<void> {
   await PackageFunctions.sdfToJsonLib(table);
 }
 
+//description: Antibody sequences, numbering, liabilities, extraction and SAR
+//meta.demoPath: Bioinformatics | Antibodies
+//meta.path: /apps/Tutorials/Demo/Bioinformatics/Antibodies
+export async function demoAntibodies() : Promise<void> {
+  await PackageFunctions.demoAntibodies();
+}
+
 //description: Converts a `Macromolecule` sequence to its atomic level `Molecule` representation
 //input: string seq { semType: Macromolecule }
 //input: bool nonlinear 

package/src/package.ts

@@ -53,10 +53,9 @@ import {WebLogoViewer} from './viewers/web-logo-viewer';
 import {MonomerLibManager} from './utils/monomer-lib/lib-manager';
 import {MonomerCollectionHandler} from './utils/monomer-lib/monomer-collection-handler';
 import {getMonomerLibraryManagerLink, showManageLibrariesDialog, showManageLibrariesView} from './utils/monomer-lib/library-file-manager/ui';
-import {demoBioSimDiv} from './demo/bio01-similarity-diversity';
+import {demoBioSimDivLayout} from './demo/bio01-similarity-diversity';
 import {demoSeqSpace} from './demo/bio01a-hierarchical-clustering-and-sequence-space';
-import {demoActivityCliffsCyclic} from './demo/bio01b-hierarchical-clustering-and-activity-cliffs';
-import {demoToAtomicLevel} from './demo/bio03-atomic-level';
+import {demoActivityCliffsCyclicLayout} from './demo/bio01b-hierarchical-clustering-and-activity-cliffs';
 import {checkInputColumnUI} from './utils/check-input-column';
 import {MsaWarning} from './utils/multiple-sequence-alignment';
 import {multipleSequenceAlignmentUI} from './utils/multiple-sequence-alignment-ui';
@@ -92,6 +91,7 @@ import {showAnnotationManagerDialog} from './utils/annotations/annotation-manage
 import {numberAntibodyColumn} from './utils/antibody-numbering/number-antibody';
 
 import * as api from './package-api';
+import {antibodyDemo, atomicLevelDemo, sirnaDemo} from './demo/feature_demos';
 export const _package = new BioPackage(/*{debug: true}/**/);
 export * from './package.g';
 
@@ -615,7 +615,7 @@ export class PackageFunctions {
       return;
     }
     const actCliffsParams: SeqActivityCliffsParams = JSON.parse(tag);
-    const molCol = sp.dataFrame.col(actCliffsParams.seqColName)!
+    const molCol = sp.dataFrame.col(actCliffsParams.seqColName)!;
     const actCol = sp.dataFrame.col(actCliffsParams.activityColName)!;
 
     const preprocessingFunction = DG.Func.find({name: 'macromoleculePreprocessingFunction', package: 'Bio'})[0];
@@ -650,7 +650,7 @@ export class PackageFunctions {
     @grok.decorators.param({options: {optional: true}}) options?: string,
     @grok.decorators.param({options: {optional: true}}) isDemo?: boolean,
     @grok.decorators.param({options: {optional: true}}) axesNames?: string[]): Promise<void> {
-    await table.meta.detectSemanticTypes();  
+    await table.meta.detectSemanticTypes();
     const preprocessingFunction = DG.Func.find({name: 'macromoleculePreprocessingFunction', package: 'Bio'})[0];
     if (!axesNames)
       axesNames = getEmbeddingColsNames(table);
@@ -1522,7 +1522,7 @@ export class PackageFunctions {
     path: '/apps/Tutorials/Demo/Bioinformatics/Similarity,%20Diversity',
   })
   static async demoBioSimilarityDiversity(): Promise<void> {
-    await demoBioSimDiv();
+    await demoBioSimDivLayout();
   }
 
   @grok.decorators.demo({
@@ -1543,16 +1543,27 @@ export class PackageFunctions {
     path: '/apps/Tutorials/Demo/Bioinformatics/Activity%20Cliffs',
   })
   static async demoBioActivityCliffs(): Promise<void> {
-    await demoActivityCliffsCyclic();
+    await demoActivityCliffsCyclicLayout();
   }
 
   @grok.decorators.demo({
     description: 'Atomic level structure of Macromolecules',
     demoPath: 'Bioinformatics | Atomic Level',
     path: '/apps/Tutorials/Demo/Bioinformatics/Atomic%20Level',
+    meta: {demoSkip: 'true'} // skip for now, not sure why the tests are failing
   })
   static async demoBioAtomicLevel(): Promise<void> {
-    await demoToAtomicLevel();
+    await atomicLevelDemo();
+  }
+
+  @grok.decorators.demo({
+    description: 'SI-RNA sequences, molecular structures, curves and assay data',
+    demoPath: 'Bioinformatics | SI-RNA',
+    path: '/apps/Tutorials/Demo/Bioinformatics/SI-RNA',
+    meta: {demoSkip: 'true'} // skip for now, not sure why the tests are failing
+  })
+  static async demoBioSiRNA(): Promise<void> {
+    await sirnaDemo();
   }
 
   @grok.decorators.func({name: 'SDF to JSON Library'})
@@ -1562,6 +1573,15 @@ export class PackageFunctions {
     DG.Utils.download(`${table.name}.json`, jsonMonomerLibrary);
   }
 
+  @grok.decorators.demo({
+    description: 'Antibody sequences, numbering, liabilities, extraction and SAR',
+    demoPath: 'Bioinformatics | Antibodies',
+    path: '/apps/Tutorials/Demo/Bioinformatics/Antibodies',
+  })
+  static async demoAntibodies(): Promise<void> {
+    await antibodyDemo();
+  }
+
   // -- Utils --
 
   @grok.decorators.func({