make new resource markdown (resource migration 2/3)

gatsby/schema/base.gql

@@ -30,6 +30,7 @@ type Resource implements Node {
     description: String
     link: String
     readmeLink: String
+    file: String
     status: String
     date: Date @dateformat
     tags: [String!]

src/cms/widgets/VariableResourceWidget/constants.ts

@@ -1,4 +1,5 @@
 import { TypeConfig } from "../VariableTypeWidget/types";
+import { RESOURCE_TYPES } from "../../../constants/resourceTypes";
 
 const SOFTWARE_STATUS_OPTIONS = [
     "Public",
@@ -17,7 +18,7 @@ const DATASET_STATUS_OPTIONS = [
 // defaults to name, description, link.
 export const VARIABLE_TYPE_RESOURCE_CONFIG: TypeConfig[] = [
     {
-        value: "softwareTool",
+        value: RESOURCE_TYPES.SOFTWARE_TOOL,
         label: "Software Tool",
         fields: [
             {
@@ -34,7 +35,7 @@ export const VARIABLE_TYPE_RESOURCE_CONFIG: TypeConfig[] = [
         ],
     },
     {
-        value: "dataset",
+        value: RESOURCE_TYPES.DATASET,
         label: "Dataset",
         fields: [
             {
@@ -46,12 +47,12 @@ export const VARIABLE_TYPE_RESOURCE_CONFIG: TypeConfig[] = [
         ],
     },
     {
-        value: "protocolLink",
+        value: RESOURCE_TYPES.PROTOCOL_LINK,
         label: "Protocol (Link)",
         fields: [],
     },
     {
-        value: "protocolFile",
+        value: RESOURCE_TYPES.PROTOCOL_FILE,
         label: "Protocol (File)",
         fields: [
             {
@@ -63,7 +64,7 @@ export const VARIABLE_TYPE_RESOURCE_CONFIG: TypeConfig[] = [
         ],
     },
     {
-        value: "cellLine",
+        value: RESOURCE_TYPES.CELL_LINE,
         label: "Cell Line",
         fields: [],
     },

src/constants/resourceTypes.ts

@@ -0,0 +1,9 @@
+export const RESOURCE_TYPES = {
+    SOFTWARE_TOOL: "softwareTool",
+    DATASET: "dataset",
+    PROTOCOL_LINK: "protocolLink",
+    PROTOCOL_FILE: "protocolFile",
+    CELL_LINE: "cellLine",
+} as const;
+
+export type ResourceType = (typeof RESOURCE_TYPES)[keyof typeof RESOURCE_TYPES];

src/graphql/fragments.ts

@@ -1,7 +1,8 @@
 import { graphql } from "gatsby";
 
-export const ResourceFieldsBase = graphql`
-    fragment ResourceFields on Resource {
+export const SoftwareToolResourceFields = graphql`
+    fragment SoftwareToolResourceFields on Resource {
+        slug
         type
         name
         description
@@ -11,3 +12,60 @@ export const ResourceFieldsBase = graphql`
         date
     }
 `;
+
+export const DatasetResourceFields = graphql`
+    fragment DatasetResourceFields on Resource {
+        slug
+        type
+        name
+        description
+        link
+        status
+        date
+    }
+`;
+
+export const CellLineResourceFields = graphql`
+    fragment CellLineResourceFields on Resource {
+        slug
+        type
+        name
+        link
+    }
+`;
+
+export const ProtocolLinkResourceFields = graphql`
+    fragment ProtocolLinkResourceFields on Resource {
+        slug
+        type
+        name
+        description
+        link
+    }
+`;
+
+export const ProtocolFileResourceFields = graphql`
+    fragment ProtocolFileResourceFields on Resource {
+        slug
+        type
+        name
+        description
+        link
+        file
+    }
+`;
+
+/**
+ * Composite fragment for querying mixed resource lists.
+ * Results include all fields across all resource types;
+ * use the `type` field to discriminate at runtime.
+ */
+export const ResourceFields = graphql`
+    fragment ResourceFields on Resource {
+        ...SoftwareToolResourceFields
+        ...DatasetResourceFields
+        ...CellLineResourceFields
+        ...ProtocolLinkResourceFields
+        ...ProtocolFileResourceFields
+    }
+`;

src/pages/ideas/2025-10-24-how-do-the-number-and-size-of-holes-in-the-basement-membrane-change-with-time-during-emt-induction.md

@@ -3,6 +3,8 @@ templateKey: idea-post
 title: How do the number and size of holes in the basement membrane change with
   time during EMT induction
 introduction: Needs background
+resources:
+  - released-emt-dataset
 materialsAndMethods:
   dataset: Released EMT dataset
 nextSteps: Need to be filled out

src/pages/ideas/2025-10-29-relate-cell-cell-junction-remodeling-to-migration-onset.md

@@ -1,6 +1,8 @@
 ---
 templateKey: idea-post
 title: Relate cell-cell junction remodeling to migration onset
+resources:
+  - released-emt-dataset
 materialsAndMethods:
   dataset: Released EMT dataset
 program:

src/pages/ideas/2026-02-06-compare-actin-filament-compression-between-different-fiber-scale-simulators.md

@@ -31,6 +31,8 @@ preliminaryFindings:
       caption: An unrelated image from our website showing lots and lots of cells.
 resources:
   - test-software-tool
+  - simularium
+  - actin-compression-simulation-dataset
 materialsAndMethods:
   dataset: Actin compression simulation dataset
   software:

src/pages/ideas/dev-example.md

@@ -5,6 +5,8 @@ preliminaryFindings:
     (rapid local changes in junction length and intensity) increases ~30–60
     minutes before migration onset in a subset of fields of view. Here is a link
     for no reason: [link](https://allencell.org/).
+    minutes before migration onset in a subset of fields of view. Here is a link
+    for no reason: [link](https://allencell.org/).
   figures:
     - type: imageFile
       file: /img/228469011.jpg
@@ -29,6 +31,11 @@ introduction: >
 resources:
   - cell-line-resources
   - test-software-tool
+  - simularium
+  - timelapse-feature-explorer
+  - released-emt-dataset
+  - aics-42
+  - aics-67
 materialsAndMethods:
   dataset: Released EMT dataset
   protocols: null

src/pages/resource/60x-timelapse-images-of-tagged-lines-after-emt-sandwich-dataset.md

@@ -0,0 +1,8 @@
+---
+templateKey: resource
+name: '60x timelapse images of tagged lines "after" EMT, "sandwich" dataset'
+resourceDetails:
+  type: dataset
+  name: '60x timelapse images of tagged lines "after" EMT, "sandwich" dataset'
+  status: Preliminary
+---

src/pages/resource/actin-compression-simulation-dataset.md

@@ -0,0 +1,36 @@
+---
+templateKey: resource
+name: Actin compression simulation dataset
+resourceDetails:
+  type: dataset
+  name: Actin compression simulation dataset
+  description: |
+    ### Overview
+
+    This dataset contains simulated data of actin filaments using the monomer-scale model [ReaDDy](https://github.com/simularium/readdy-models) and fiber-scale model [Cytosim](https://github.com/simularium/Cytosim).
+
+    Simulation conditions test compression of a single 500 nm actin filament at different velocities, as well as control simulations with no compression.
+
+    Compression simulations use the prefix `ACTIN_COMPRESSION_VELOCITY`; control simulations use the prefix `ACTIN_NO_COMPRESSION`.
+
+    Compression simulation keys include the following:
+
+    - `0047` = 4.7 μm/s
+    - `0150` = 15 μm/s
+    - `0470` = 47 μm/s
+    - `1500` = 150 μm/s
+
+    For _ReaDDy_, the actin filament is composed of particles, each representing an actin monomer, initialized based on measurements from an actin crystal structure. Compression was implemented by linearly displacing the three monomers at the pointed end for one time step and then allowing the structure to relax for nine time steps, until the fiber was compressed to 350 nm. Each simulation condition contains 5 replicates.
+
+    For _Cytosim_, the actin filament is modeled as a 500 nm fiber anchored by two fiber-binding linkers spaced 10 nm apart at each end. The linkers on one of the ends were translated linearly for one time step and allowed to relax for nine time steps, until the fiber was compressed to 350 nm. Each simulation condition contains 5 replicates, with replicates corresponding to random seeds 1, 2, 3, 4, and 5.
+
+    ### Usage
+
+    For documentation on how to use and interact with this dataset please refer to [https://docs.quiltdata.com/walkthrough/getting-data-from-a-package](https://docs.quiltdata.com/walkthrough/getting-data-from-a-package).
+
+    ### License
+
+    For questions on licensing please refer to [https://www.allencell.org/terms-of-use.html](https://www.allencell.org/terms-of-use.html).
+  link: https://open.quiltdata.com/b/allencell/tree/aics/subcellular_model_simulations/subcellular_model_simulations_actin_comparison/
+  status: Public
+---

src/pages/resource/aics-42.md

@@ -0,0 +1,8 @@
+---
+templateKey: resource
+name: AICS-42
+resourceDetails:
+  type: cellLine
+  name: AICS-42
+  link: https://allencell.org/cell-catalog
+---

src/pages/resource/aics-67.md

@@ -0,0 +1,8 @@
+---
+templateKey: resource
+name: AICS-67
+resourceDetails:
+  type: cellLine
+  name: AICS-67
+  link: https://allencell.org/cell-catalog
+---

src/pages/resource/emc.md

@@ -0,0 +1,9 @@
+---
+templateKey: resource
+name: "EMC"
+resourceDetails:
+  type: dataset
+  name: "EMC"
+  description: We have some preliminary data on different ECM to drive lumenoid formation
+  status: Preliminary
+---

src/pages/resource/index.tsx

@@ -3,31 +3,61 @@ import { Helmet } from "react-helmet-async";
 
 import { Link, PageProps, graphql } from "gatsby";
 
-const ResourcesPage: React.FC<PageProps<Queries.ResourcesIndexQueryQuery>> = ({
+
+type ResourceNode = { slug: string; name: string | null; description?: string | null };
+
+function renderResourceList(nodes: ResourceNode[]) {
+    if (!nodes.length) return null;
+    return (
+        <ul>
+            {nodes.map((node) => (
+                <li key={node.slug}>
+                    <Link to={node.slug}>{node.name}</Link>
+                    {node.description && <p>{node.description}</p>}
+                </li>
+            ))}
+        </ul>
+    );
+}
+
+const resourceSections: {
+    title: string;
+    keys: (keyof Omit<Queries.ResourcesIndexQuery, "site">)[];
+}[] = [
+    { title: "Software", keys: ["softwareResources"] },
+    { title: "Datasets", keys: ["datasetResources"] },
+    { title: "Cell Lines", keys: ["cellLineResources"] },
+    {
+        title: "Protocols",
+        keys: ["protocolLinkResources", "protocolFileResources"],
+    },
+];
+
+const ResourcesPage: React.FC<PageProps<Queries.ResourcesIndexQuery>> = ({
     data,
 }) => {
-    const { allResource, site } = data;
-
-    if (!allResource || !site) {
+    if (!data.site) {
         return <p>Data not found.</p>;
     }
 
-    const { nodes } = allResource;
-    const title = site.siteMetadata?.title || "Title";
+    const title = data.site.siteMetadata?.title || "Title";
     return (
         <section>
             <Helmet title={`Resources | ${title}`} />
             <div>
                 <h1>Resources</h1>
-                <ul>
-                    {nodes.map((node) => (
-                        <li key={node.slug}>
-                            <Link to={node.slug}>{node.name}</Link>
-                            {node.description && <p>{node.description}</p>}
-                            {node.type && <p>{node.type}</p>}
-                        </li>
-                    ))}
-                </ul>
+                {resourceSections.map(({ keys, title: sectionTitle }) => {
+                    const nodes = keys.flatMap(
+                        (key) => data[key]?.nodes ?? []
+                    );
+                    if (!nodes.length) return null;
+                    return (
+                        <React.Fragment key={sectionTitle}>
+                            <h2>{sectionTitle}</h2>
+                            {renderResourceList(nodes)}
+                        </React.Fragment>
+                    );
+                })}
             </div>
         </section>
     );
@@ -36,16 +66,41 @@ const ResourcesPage: React.FC<PageProps<Queries.ResourcesIndexQueryQuery>> = ({
 export default ResourcesPage;
 
 export const resourcePageQuery = graphql`
-    query ResourcesIndexQuery {
+    query ResourcesIndex {
         site {
             siteMetadata {
                 title
             }
         }
-        allResource {
+        datasetResources: allResource(filter: { type: { eq: "dataset" } }) {
+            nodes {
+                ...DatasetResourceFields
+            }
+        }
+        softwareResources: allResource(
+            filter: { type: { eq: "softwareTool" } }
+        ) {
+            nodes {
+                ...SoftwareToolResourceFields
+            }
+        }
+        cellLineResources: allResource(filter: { type: { eq: "cellLine" } }) {
+            nodes {
+                ...CellLineResourceFields
+            }
+        }
+        protocolLinkResources: allResource(
+            filter: { type: { eq: "protocolLink" } }
+        ) {
+            nodes {
+                ...ProtocolLinkResourceFields
+            }
+        }
+        protocolFileResources: allResource(
+            filter: { type: { eq: "protocolFile" } }
+        ) {
             nodes {
-                slug
-                ...ResourceFields
+                ...ProtocolFileResourceFields
             }
         }
     }

src/pages/resource/released-emt-dataset.md

@@ -0,0 +1,10 @@
+---
+templateKey: resource
+name: Released EMT dataset
+resourceDetails:
+  type: dataset
+  name: Released EMT dataset
+  description: Description for released EMT dataset in the markdown file for the dataset.
+  link: https://www.biorxiv.org/content/10.1101/2024.08.16.608353v1.full
+  status: Public
+---