Test simple model and data repository using bio-ontology annotations.
See the file "Repository notes.docx" for a bit more info.

Section 1: Images

Annotations are included as comments within the jpeg files. In addition, since it is unclear if Google will actually examine the embeded annotations, the images are also included on individual web pages with the annotations.

• Somitogenesis image somitogenesis_image.jpg.
  (Experimental image from Duband et al. 1987.)
  
• Image of CC3D model of somitogenesis somitogenesis_image_CC3D_model.jpg
  (Image from JM Belmonte, SD Hester, S Clendenon, JS Gens, JA Glazier)
  

Section 2: Python Scripts

Annotations are included as comments within files.

• 3D multi-cell simulation of tumor growth and angiogenesis.txt
• Need CC3D script (annotated) for nutrophil chasing bacterium.

Section 3: Scripts embedded in HTML documents

Annotations are included as comments within the files.

• 3D multi-cell simulation of tumor growth and angiogenesis.html

Section 4: Movies

• Annotations here, none in file.

  Neutrophil chasing a bacterium UniProt Taxonomy Database NEWT: NEWT:2 Bacteria Cell Type Ontology CL: CL:0000775 neutrophil "polynuclear neutrophilic leucocyte" neutrocyte Foundational Model of Anatomy FMA: FMA:62860 "Polymorphonuclear leukocyte" FMA:82840 embryonic cell Gene Ontology GO: GO:0006909 phagocytosis GO:0060326 "cell chemotaxis" GO:0048870 "cell motility" Protein Ontology PRO: Biological Imaging Methods FBbi: FBbi:00000265 micrograph FBbi:00000267 animation HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY Indiana University Bloomington University of Washington

  Crawling_Neutrophil_chasing_bacterium.mp4

  
  
• Annotations in "credits" of a WMV video file Crawling_Neutrophil_chasing_bacterium_annot.wmv.
• Need Movie of CC3D model of neutrophil chasing bacterium.

Section 5: Links to other repositories

• The Indiana University Bloomington Site.
• The University of Washington Site.

Biocomplexity Institute
Indiana University
4 March 2011