Repository notes Started: 2/28/2011 The goal is a distributed database of images, biological data and models. The hope is that if the files are adequately annotated, using an agreed upon set of reference ontologies, then the distributed files can be located via a Google search. The user should not need to know where the files are located. Furthermore, the annotation syntax should be as non-restrictive as possible and annotation of a file should not change the usability of the file for its original porpose. Longer range goals might include annotation styles linking annotations to entities in the data file. For example, in a CC3D model linking cell names and/or type IDs to annotations. Annotations in an SBML file that link variable names to protein names. File and data types: Major issue is that the file type has to be "crawlable" and "indexable" by Google. File types to try include: Any plain text files including computational scripts in python, C++ etc. Tab or csv data table files containing numeric values (e.g., from ToxCast, a high throughput assay, or an archive of common physiochemical parameters like affinity constants, diffusion rates and the like). MSWord, PowerPoint and PDF files. HTML files. Images (jpg, gif …) either as photographs (or micrographs) of tissues, cells etc. or images generated as output of a modeling program. Movies of tissues, cells etc. or images generated as from the output of a modeling program. For the image type of files it would be nice if Google would index the file format's native annotation block. That would allow the annotation to actually live in the file. (See the file somatogenesis_image_CC3D_model.jpg for an example.) Unfortunately, it doesn't look like Google does that. To associate annotation with an image file we need to place both in an HTML (or PDF or …) file.
Transcript
Repository notesStarted: 2/28/2011
The goal is a distributed database of images, biological data and models. The hope is that if the files are adequately annotated, using an agreed upon set of reference ontologies, then the distributed files can be located via a Google search. The user should not need to know where the files are located. Furthermore, the annotation syntax should be as non-restrictive as possible and annotation of a file should not change the usability of the file for its original porpose.
Longer range goals might include annotation styles linking annotations to entities in the data file. For example, in a CC3D model linking cell names and/or type IDs to annotations. Annotations in an SBML file that link variable names to protein names.
File and data types:Major issue is that the file type has to be "crawlable" and "indexable" by Google. File types to try include:
Any plain text files including computational scripts in python, C++ etc. Tab or csv data table files containing numeric values (e.g., from ToxCast, a high throughput
assay, or an archive of common physiochemical parameters like affinity constants, diffusion rates and the like).
MSWord, PowerPoint and PDF files. HTML files. Images (jpg, gif …) either as photographs (or micrographs) of tissues, cells etc. or images
generated as output of a modeling program. Movies of tissues, cells etc. or images generated as from the output of a modeling program.
For the image type of files it would be nice if Google would index the file format's native annotation block. That would allow the annotation to actually live in the file. (See the file somatogenesis_image_CC3D_model.jpg for an example.) Unfortunately, it doesn't look like Google does that. To associate annotation with an image file we need to place both in an HTML (or PDF or …) file.
Annotations:The goal is to include the annotation without interfering with the native file format. Annotations in code or script files should live inside comment delimiters suitable for the particular language. In non-code files (like HTML, word, csv) this isn't as much of an issue. Major issue is that there needs to be an agreed upon set of reference ontologies so that end users know which ontologies to search for query terms. A secondary issue is that a user friendly tool for finding terms in the reference ontologies would be very helpful.
Possible Reference Ontologies:Major issue is multi-species requirements. FMA is human can it be adequately used for other species? In some cases yes, in many cases no.
Ontologies / vocabularies searchable by the querying tools marked with *.
Mammalian body parts, locations and processes: FMA*(http://sig.biostr.washington.edu/projects/fm/FME/index.html)
Non-mammalian body parts: ? Gene Processes: GO*
(http://amigo.geneontology.org/cgi-bin/amigo/go.cgi) Gene and protein names: PRO*
(http://pir.georgetown.edu/pro/) Small molecules: ChEBI*
(http://www.nlm.nih.gov/mesh/MBrowser.html) Another Catch-all Reference Ontology: UMLS
(http://www.nlm.nih.gov/research/umls/ don't know of any online search engines.)
Possible user tools for querying the reference ontologies:http://www.ebi.ac.uk/ontology-lookup/ (doesn't include UMLS or MeSH!)http://bioportal.bioontology.org/
Annotation Style:The key requirement is that the annotation contains the terms, IDs and reference ontology identifier. For example "FMA:82840 embryonic cell" identifies the ontology (FMA), ID (82840) and the term name ("embryonic cell"). There should be a unique ontology identifier for the typical ontologies so that the ID and ontology can be closely linked, perhaps to a single "word" level, such as "FMA:82840". An explicit listing of the ontologies being used might also be useful. It may be advantageous to have a text template that lists the major types of annotations that might be included along with the suitable reference ontology names. The template is not part of the data structure, it is simply meant to help the annotator work through the process in an orderly fashion. Major sections of the annotation template might be something along the lines of:
1. Process being modeled/studied (examples: tumor growth, immune response, embryogenesis)
2. Tissues in the model/system (examples: liver, mammary tumor)3. Cells in the model/system (examples: macrophage, neuron, epithelium)4. Non-cell structures in the model/system (examples: bone, basement membrane)5. Genes and gene products in the model system (examples: VEGF-A, IL-1b)6. Molecules not covered by 5. (examples: oxygen, glucose, potassium ions)7. Processes and behaviors of the things (cells, genes, tissues) in the model/system (examples:
gene expression, cell growth, division and death, diffusion)
Some annotated files:Jpeg image from Julio & Susan’s poster of somitogenesis. Annotations added to the jpeg file somitogenesis_image.jpg:
Somitogenesis imageFoundational Model of Anatomy FMA: FMA:69068 embryo FMA:82840 embryonic cellGene Ontology GO: GO:0009790 embryogenesis GO:0009792 embryo development ending in birth or egg hatching GO:0016055 Wnt receptor signaling pathwayProtein Ontology PRO: PRO:000017443 protein Wnt-3aBiological Imaging Methods FBbi: FBbi:00000265 micrograph MeSH:A16.504.660.750 somitesHERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORYIndiana University BloomingtonUniversity of Washington
CC3D (CompuCell3D) Result Image CC3D_somitogenesis_image.jpg:
Somitogenesis computational model imageFoundational Model of Anatomy FMA: FMA:69068 embryo FMA:82840 embryonic cellGene Ontology GO: GO:0009790 embryogenesis GO:0009792 embryo development ending in birth or egg hatching GO:0016055 Wnt receptor signaling pathwayProtein Ontology PRO: PRO:000017443 protein Wnt-3aEMBRACE Ontology for Data and Methods EDAM: EDAM:0000950 Biological modelMedical Subject Heading MeSH: MeSH:E05.599 Models, Theoretical MeSH:E05.599.395 Models, Biological MeSH:L01.224.160 Computer Simulation MeSH:A16.504.660.750 somitesAuthors: Susan Hester, Julio Belmonte Indiana University, BloomingtonComputational Platform: CompuCell3D CC3D
HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORYIndiana University BloomingtonUniversity of Washington
MP4 Movie file: Crawling_Neutrophil_chasing_bacterium.mp4
Neutrophil chasing a bacteriumUniProt Taxonomy Database NEWT: NEWT:2 BacteriaCell Type Ontology CL: CL:0000775 neutrophil "polynuclear neutrophilic leucocyte" neutrocyteFoundational Model of Anatomy FMA: FMA:62860 "Polymorphonuclear leukocyte" FMA:82840 embryonic cellGene Ontology GO: GO:0006909 phagocytosis GO:0060326 "cell chemotaxis" GO:0048870 "cell motility"
3/8/2011Google finds the pages using, e.g., "CHEBIO:15379 cc3d herbs and jims …"
But problem with the svn paths FIXED
MeSH terms used for typical biomodels.
Abbas et al. Tumor Niko et al. TumorCardiac ventricular action
potentialPLoS One. 2009 Oct 16;4(10):e7190."3D multi-cell simulation of tumor growth and angiogenesis" Shirinifard A, Gens JS, Zaitlen BL, Popławski NJ, Swat M, Glazier JA.
PLoS One. 2010 May 26;5(5):e10641."Front instabilities and invasiveness of simulated 3D avascular tumors" Poplawski NJ, Shirinifard A, Agero U, Gens JS, Swat M, Glazier JA.
Circ Res. 1994 Jun;74(6):1071-96."A dynamic model of the cardiac ventricular action potential. I. Simulations of ionic currents and concentration changes" Luo CH, Rudy Y.
3/16/2011Google with "BIOMD:0000000201 BIOMODELS" returns one link, the correct one to the biomodels DB.
Google with "GO:0007219 biomodels" tags from within the SBML file doesn't find the Biomodels file at the BioModelsDB but does find a pdf version of the model at CalTech. (Three links total returned)
Google with "GO:0016055 PRO:000017443 HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY" find the somitogenesis files in HERBS/JIMS but not the original or re-annotated SBML file. (Google hasn't indexed it yet?)
3/23/2011Still don't seem to find the biomodel files. Used the Biomodels DB tool to create a PDF summary description of the model file (BIOMD0000000201.pdf) and added it to the repository.
4/5/2011Checked again using "GO:0008543 HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY" and "urn:miriam:obo.go:GO:0008543 HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY", still not finding the original BioModels or the LaTex versions of the BioModels file. Perhaps Google doesn't index terms such as "urn:miriam:obo.go:GO:0008543"?
Added a table to the top of the BioModels pdf file with:
------------- end added annotations jps --------------------------------
The new pdf file is BIOMD0000000201_mod.pdf
Fixed misspelling of "biological" in several of the html file's keywords. Gave the various HTML pages suitable HTML <title> tags.
4/7/2011Google with:
"GO:0008543 HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY"
"Wnt receptor signaling pathway HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY"
"urn:miriam:obo.go:GO%3A0008543 HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY"
"urn:miriam:obo.go:GO:0008543 HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY"
"urn Miriam obo go GO:0008543 HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY"
"urn Miriam obo go GO 0008543 HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY"
No hits. Wait a couple more days and try again.
Multiple data sources should share a common biological description.("C:\Users\James Sluka\Desktop\Biocomplexity\Ontologies\Common markup across multiple data source.pptx")
There is a newer version of the above figure (with an SBML model)
4/20/11From Herbert:
James, sorry to take so long but I now have a url for you:
This has a list of 10 biomodels in sbml and pdf format. To each sbml file I added this text: "HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY Indiana University Bloomington University of Washington"
Is there anything else I need to do?
Herb
Added his list of files to the index file (document_list_IU.html) and sent him a copy.
8/2/2011
FOAF annotations in RDF so Google will indexA FOAF file in RDF:
My version using urn:Miriam:obo tags (GO:0008543 is FGFr signaling pathway). Not sure if the GO:0008543 part should use something else for the ":". Not sure if the Miriam markup should be the "about", the "name" or something else. Same with the "HERBS AND JIMS…"
Added to the top of the BIOMD0000000201_mod.xml file and saved as BIOMD0000000201_mod_FOAF.xml.
8/8/2011Added biomodel with the DBBR annotations in the <notes> block of the header.
BIOMD0000000201_DBBR_notes.xml
8/10/2011Google q's for the BIOMD0000000201_DBBR_notes.xml:urn:miriam:interpro:IPR013284 Distributed Biodata and Biomodel Resource IPR013284 Distributed Biodata and Biomodel Resource
Beta-catenin Distributed Biodata and Biomodel Resource Distributed Biodata and Biomodel Resource
No hits yet
Created Word and Excel versions of the raw XML BIOMD0000000201.xml file. Also created versions of the DBBR annotated file.
Q: urn:miriam:interpro:IPR013284 Distributed Biodata and Biomodel Resource(IPR013284 is Beta-catenin) 4 hits total, first hit is the repository_notes.doc file.BIOMD0000000201.docx noBIOMD0000000201.pdf noBIOMD0000000201.xlsx noBIOMD0000000201.xml noBIOMD0000000201_DBBR_notes.docx YesBIOMD0000000201_DBBR_notes.xlsx YesBIOMD0000000201_DBBR_notes.xml YesBIOMD0000000201_mod.pdf noBIOMD0000000201_mod.xml noBIOMD0000000201_mod_FOAF.xml no
Q: IPR013284 Distributed Biodata and Biomodel ResourceFinds the same three files
Q: Beta-catenin Distributed Biodata and Biomodel ResourceFinds the same three plus five non-DBBR files (relevant hits are all first)
Note that no files are found directly in the BioModels database!
5 April 2012: the sentence above no longer appears to be true. There are now static pages, e.g.,http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=ModelMonth%2F2009-04
<!-- This model was downloaded from BioModels Database --><!-- Thu Mar 03 22:08:56 GMT 2011 --><!-- http://www.ebi.ac.uk/biomodels/ -->
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" metaid="metaid_0000001" level="2" version="3"> <model metaid="metaid_0000002" id="Goldbeter2008_Somite_Segmentation_Clock_Notch_Wnt_FGF"> <notes>########## Distributed Biodata and Biomodel Resource Annotations ########################## In this file Ontology Term URN Ontology Term Synonyms## DBBR: Rasi urn:miriam:interpro:IPR001806 Small GTPase superfamily## DBBR: D urn:miriam:interpro:IPR003351 Dishevelled protein## DBBR: N urn:miriam:interpro:IPR008297 Notch## DBBR: ERKa urn:miriam:interpro:IPR008349 ERK1/2 MAP kinase## DBBR: Bp urn:miriam:interpro:IPR013284 Beta-catenin## DBBR: Fgf urn:miriam:interpro:IPR017338 Fibroblast growth factor, 15/19/21## DBBR: MF urn:miriam:interpro:IPR017374 Fringe## DBBR: Bp urn:miriam:kegg.compound:C00562 Phosphoprotein## DBBR: urn:miriam:kegg.pathway:ko04330 Notch signaling pathway## DBBR: Rasa urn:miriam:obo.chebi:CHEBI%3A15996 GTP Guanosine 5'-triphosphate## DBBR: Rasi urn:miriam:obo.chebi:CHEBI%3A17552 GDP Guanosine 5'-diphosphate, Guanosine diphosphate## DBBR: urn:miriam:obo.chebi:CHEBI%3A33699 messenger RNA## DBBR: urn:miriam:obo.go:GO%3A0001756 somitogenesis formation of mesodermal clusters## DBBR: cytosol urn:miriam:obo.go:GO%3A0005829 cytosol## DBBR: urn:miriam:obo.go:GO%3A0006402 mRNA catabolic process mRNA breakdown, mRNA catabolism, mRNA degradation## DBBR: urn:miriam:obo.go:GO%3A0006412 translation protein biosynthesis, protein formation## DBBR: urn:miriam:obo.go:GO%3A0006468 protein phosphorylation protein amino acid phosphorylation## DBBR: urn:miriam:reactome:REACT_11045.1 Pathway: Signaling by Wnt (Homo sapiens)## DBBR: urn:miriam:reactome:REACT_11065.1 Pathway: Beta-catenin phosphorylation cascade (Homo sapiens)## DBBR: urn:miriam:reactome:REACT_1482.4 Pathway: ERK activation (Homo sapiens)## DBBR: urn:miriam:reactome:REACT_299.2 Pathway: Signaling by Notch (Homo sapiens)## DBBR: urn:miriam:reactome:REACT_9470.2 Pathway: Signaling by FGFR (Homo sapiens)## DBBR: urn:miriam:taxonomy:32524 Amniota amniotes## DBBR: D urn:miriam:uniprot:O14640 DVL1 Segment polarity protein dishevelled homolog DVL-1 Dishevelled-1, DSH homolog 1## DBBR: Bp urn:miriam:uniprot:P35222 Catenin beta-1 Beta-catenin, CTNNB1, CTNNB## DBBR: N urn:miriam:uniprot:P46531 Notch 1 Neurogenic locus notch homolog protein 1, hN1, Translocation-associated notch protein TAN-1, Notch1, Tan1## DBBR: K urn:miriam:uniprot:P49841 GSK-3 beta Glycogen synthase kinase-3 beta, GSK3B## DBBR: MDusp urn:miriam:uniprot:Q16828 DUSP6 Dual specificity protein phosphatase 6, Dual specificity protein phosphatase PYST1, Mitogen-activated protein kinase phosphatase 3, MKP3, PYST1## DBBR: MF urn:miriam:uniprot:Q8NES3 LFNG Beta-1,3-N-acetylglucosaminyltransferase lunatic fringe, O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase## DBBR: A urn:miriam:uniprot:Q9Y2T1 AXIN2 Axin-2, Axin-like protein, Axil, Axis inhibition protein 2, Conductin
<p xmlns="http://www.w3.org/1999/xhtml">This is a model of the coupled Natch, Wnt and FGF modules as described in:<br/> <b>A. Goldbeter and O. Pourqui�</b>,
<em>Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways.</em> J Theor Biol. 2008 Jun 7;252(3):574-85, pubmed ID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/18308339">18308339</a> <br/>To uncouple the modules remove the reaction <em>MAx_trans_Xa</em> and set <em>vsFK=vsF</em>. <br/>The SBML version of the model was converted from the CellML <a href="http://www.cellml.org/models/goldbeter_pourquie_2008_version02">version</a> by Catherine Lloyd for the <a href="http://www.cellml.org/models"> CellML repository </a>.</p> <p xmlns="http://www.w3.org/1999/xhtml">This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2010 The BioModels.net Team.<br/>For more information see the <a href="http://www.ebi.ac.uk/biomodels/legal.html" target="_blank">terms of use</a>.<br/>To cite BioModels Database, please use: <a href="http://www.ncbi.nlm.nih.gov/pubmed/20587024" target="_blank">Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Nov�re N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.</a></p> </notes> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#metaid_0000002"> <dc:creator rdf:parseType="Resource"> <rdf:Bag> <rdf:li rdf:parseType="Resource"> <vCard:N rdf:parseType="Resource"> <vCard:Family>Lloyd</vCard:Family> <vCard:Given>Catherine</vCard:Given>
Test to see if Google indexes Mathematica and MatLab files. File BIOMD0000000201.xml converted to Mathematica (BIOMD0000000201_jasrnacLite2_2_mathematica.m) and MatLab (BIOMD0000000201_jasrnacLite2_2_matlab.m) using JarnacLite2.
Added DBBR annotations from BIOMD0000000201_DBBR_notes.xmlBIOMD0000000201_jasrnacLite2_2_mathematica_DBBR_notes.m (In the "Synopsis" section.)BIOMD0000000201_jasrnacLite2_2_matlab_DBBR_notes.m (% comments in the "Synopsis" section.)
9/9/2011
Google with query: (same as last time I searched)urn:miriam:interpro:IPR013284 Distributed Biodata and Biomodel Resource
Found the same 4 files (one is the word doc) as before
Google query for the somitogenesis files (using the old tag for DBBR) :FMA:82840 embryonic cell GO:0016055 Wnt receptor signaling pathway HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY
Finds just four files, all in the IU model repository (http://cbo.biocomplexity.indiana.edu/):
(There are two paths to the same directory, http://cbo.biocomplexity.indiana.edu/models/ and http://cbo.biocomplexity.indiana.edu/svn/model_repo_v0/ )
FOAF test. Looking for the FOAF annotated file BIOMD0000000201_mod_FOAF.xmlGoogle query:
HERBS AND JIMS BIG DATA AND COMPUTATIONAL MODEL REPOSITORY urn:miriam:obo.go:GO:0008543
Finds the word index doc and BIOMD0000000201_mod-2.pdf but not the FOAF marked file. Not sure if FOAF just doesn't work or if it is a syntax problem and the xmlns:foaf tag isn't working right.
Biomodels style file (local) PDF version test, looking for BIOMD0000000201.pdf.Google query (terms selected from "Table 3: Properties of each species.":
nuclear beta-catenin Notch protein Dusp6Finds 29,700 hits
So, it doesn’t find the Biomodel in the Biomodel repository but does find a couple reformatted versions (one in Jarnac and a page with the extracted table of included species).
A "light-weight" annotation blockInclude URN to naming resources, include the name in the file being annotated, include any available aliases and AKAs, include DBBR tag line
########## Distributed Biodata and Biomodel Resource Annotations ########################## In this file Ontology Term URN Ontology Term Synonyms## DBBR: Rasi urn:miriam:interpro:IPR001806 Small GTPase superfamily## DBBR: D urn:miriam:interpro:IPR003351 Dishevelled protein## DBBR: N urn:miriam:interpro:IPR008297 Notch## DBBR: ERKa urn:miriam:interpro:IPR008349 ERK1/2 MAP kinase## DBBR: Bp urn:miriam:interpro:IPR013284 Beta-catenin## DBBR: Fgf urn:miriam:interpro:IPR017338 Fibroblast growth factor, 15/19/21## DBBR: MF urn:miriam:interpro:IPR017374 Fringe## DBBR: Bp urn:miriam:kegg.compound:C00562 Phosphoprotein## DBBR: urn:miriam:kegg.pathway:ko04330 Notch signaling pathway## DBBR: Rasa urn:miriam:obo.chebi:CHEBI%3A15996 GTP Guanosine 5'-triphosphate## DBBR: Rasi urn:miriam:obo.chebi:CHEBI%3A17552 GDP Guanosine 5'-diphosphate## DBBR: urn:miriam:obo.chebi:CHEBI%3A33699 messenger RNA## DBBR: urn:miriam:obo.go:GO%3A0001756 somitogenesis formation of mesodermal clusters## DBBR: cytosol urn:miriam:obo.go:GO%3A0005829 cytosol
Columns are tab delimited. Within a column individual entries are comma delimited. Multiword entries are not quoted but imbedded commas need to be escaped. If a given entity or concept has multiple urns then each gets its own line in the table?
Column Contents Style Notes
1 File type specific comment e.g. ## DBBR:2 Label/tag for this entity in this file text
3 Ontology terms as a urn urn Often end is a numeric, e.g., urn:miriam:obo.chebi:CHEBI%3A15996
4 Ontology term official name text single name5 Pseudonym list text list list of names
4/2/2012
Added three files as test classes for OWL ontologies:
http://cbo.biocomplexity.indiana.edu/svn/model_repo_v0/pizz_jps_embed_edited_xml_in_comment.owl http://cbo.biocomplexity.indiana.edu/svn/model_repo_v0/pizz_jps_manchester.owl http://cbo.biocomplexity.indiana.edu/svn/model_repo_v0/pizz_jps.owlThe pizz_jps_embed_edited_xml_in_comment.owl file has the entire xml file "de-xml-ed" then embedded into a comment tag.
The server appears to be MIA, sent Alin an email about it. Fixed.
TO DO: Check if Google indexes any of these ontology files.
11/9/2012
Added an annotated CC3D Python script:angio_growth_steppables_08052009_01_45_36__CBOannotated.py
