Add Bican Flow Diagram

bican_flow_diagram/bican_flow_diagram.md

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+# Purpose
+The purpose of this diagram is to show how data and materials flow across the BICAN ecosystem.
+
+# Definitions
+| Node Name       | Definition                                             |
+|----------------|------------------------------------------------------|
+| NBB            | Neuro Bio Bank                                       |
+| IMS            | [Information Management Services](https://www.imsweb.com) |
+| BICAN Investigator | TODO                                               |
+| Specimen Portal | The [Specimen Portal](https://brain-specimenportal.org) focuses on tissue management from donors to brain slabs and annotated brain samples.|
+| SeqLib Portal | The [Sequence Library (SeqLib) Portal](https://brain-specimenportal.org) manages the workflow starting from tissue, all the way downstream to track data deposition to assay-dependent data-modality-specific archives.|
+| SeqCores       | TODO                                                 |
+| NeMO           | The [Neuroscience Multi-omic Archive (NeMO Archive)](https://nemoarchive.org) is a data repository specifically focused on the storage and dissemination of omic data generated from the BRAIN Initiative, SCORCH consortium and other brain research projects.|
+| Terra Alignment | TODO                                                 |
+| Data Catalog, BICAN Dashboard | A searchable [data catalog](https://knowledge.brain-map.org/data) listing all public BICCN and BICAN generated data about cell types.|
+| Knowledge Base, BICAN Cell Atlas | The Brain Cell Knowledge Base ingests and standardizes comprehensive cell type information from BICAN's development of a multimodal, multi-species brain cell atlas and disseminate that atlas as an open and interactive community resource for advancing knowledge of the brain.|
+
+# Sequence Diagram
+```mermaid
+sequenceDiagram
+    participant NBB
+    participant IMS
+    participant BICAN Investigator
+    participant Specimen Portal
+    participant SeqLib Portal 
+    participant SeqCores
+    participant NeMO
+    participant Terra Alignment
+    participant DataCatalog as Data Catalog, BICAN Dashboard
+    participant KnowledgeBase as Knowledge Base, BICAN Cell Atlas 
+
+    BICAN Investigator ->> Specimen Portal: 1. Tissue Request
+
+    Specimen Portal ->> IMS: 2. Request Forward
+    IMS ->> NBB: 2. Request Forward
+
+    IMS ->> Specimen Portal: 3. Status Update
+    NBB ->> IMS: 3. Status Update
+    NBB ->> Specimen Portal: 3. Update ROI Drawing
+    NBB ->> BICAN Investigator: 3. Tissue Shipment
+
+    BICAN Investigator ->> Specimen Portal: 4. Tissue QC Free text & Structured
+    BICAN Investigator ->> SeqLib Portal: 4.Library & Pool Generation
+
+    BICAN Investigator ->> SeqCores: 5. Library Shipment
+    SeqLib Portal ->> SeqCores: 5. SeqCore Dashboard Update & Notification 
+    SeqLib Portal ->> NeMO: 5. NeMO Dashboard Update & Notification
+
+    SeqCores ->> NeMO: 6. Fastq File Deposition
+    SeqCores ->> SeqLib Portal: 6. Run QC Metric
+
+    NeMO ->> SeqLib Portal: 7. QC Metric Update
+
+    Terra Alignment ->> NeMO: 8. Investigator validation
+
+
+    Specimen Portal -->> SeqLib Portal: Information Flow
+    Specimen Portal -->> DataCatalog: Information Flow
+    Specimen Portal -->> KnowledgeBase: Information Flow
+    SeqLib Portal -->> KnowledgeBase: Information Flow
+    SeqLib Portal -->> NeMO: Information Flow
+    NeMO -->> KnowledgeBase: Information Flow
+    NeMO -->> DataCatalog: Information Flow
+    BICAN Investigator -->> DataCatalog: Information Flow
+    DataCatalog -->> NeMO: Information Flow
+```