Registry of Standard Biological Models

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A collection of models of biological parts that can be freely reused and composed with each other to produce more complex models. A draft implementation of the registry is underway and collaborators are being sought.
Talk to us at - BioSysBio 2007, SB3.0, and iGEM Jamboree Workshop 2007
Goals
  • To contribute to the Open Source Synthetic Biology effort.
  • To store, curate and support models related to physical Biobricks.
  • To drive and guide the experimental characterization of BioBricks.
  • To enable the reuse of modular part models.
  • To provide a forum for modelers to contribute to the BioBricks effort.
Activities
  • Planning the architecture of a registry of standard biological models.
  • Building a collection of standard biological models.
  • Define a modeling description language that is:
    • Machine readable
    • Capable of describing gene expression networks
    • Modular (standardized defined inputs/ouputs)
    • Hierarchical (models are composable)
    • Capable of describing models that can be related to experimental data.

Recent edits:
List of abbreviations:
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17 February 2019

     16:06 (User creation log) . . User account Vampiresoap (talk | contribs) was created by Yar (talk | contribs) and password was sent by email ‎

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Leanne Kuwahara-Week 4/5‎‎ (23 changes | history) . . (-1,632). . [Leannekuwahara‎ (23×)]

     

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(cur | prev) . . (-94). . Leannekuwahara (talk | contribs) (Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes: edited yeastract protocol)

     

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(cur | prev) . . (-262). . Leannekuwahara (talk | contribs) (Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes (Tuesday, Feb. 19): added purpose)

     

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(cur | prev) . . (+12). . Leannekuwahara (talk | contribs) (Protocol: ital purpose)

     

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(cur | prev) . . (0). . Leannekuwahara (talk | contribs) (Calculate the Benjamini & Hochberg p-value Correction: moved location of sanity check step)

     

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(cur | prev) . . (+90). . Leannekuwahara (talk | contribs) (Calculate the Benjamini & Hochberg p-value Correction: added sanity check)

     

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(cur | prev) . . (-2,697). . Leannekuwahara (talk | contribs) (Sanity Check: Number of genes significantly changed: removed sanity check from protocol (in results))

     

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(cur | prev) . . (+2,131). . Leannekuwahara (talk | contribs) (Results: added sanity check)

     

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(cur | prev) . . (+47). . Leannekuwahara (talk | contribs) (Calculate the Benjamini & Hochberg p-value Correction: added filename)

     

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(cur | prev) . . (-23). . Leannekuwahara (talk | contribs) (Materials: edited materials)

     

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(cur | prev) . . (+194). . Leannekuwahara (talk | contribs) (Clustering and GO Term Enrichment with stem: added purpose for clustering)

     

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(cur | prev) . . (+63). . Leannekuwahara (talk | contribs) (Materials: added filename for GO table)

     

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(cur | prev) . . (+980). . Leannekuwahara (talk | contribs) (Results: added GO definitions)

     

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(cur | prev) . . (+13). . Leannekuwahara (talk | contribs) (Clustering and GO Term Enrichment with stem: updated stem analysis)

     

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(cur | prev) . . (-29). . Leannekuwahara (talk | contribs) (Clustering and GO Term Enrichment with stem: edited stem analysis)

     

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(cur | prev) . . (-117). . Leannekuwahara (talk | contribs) (Clustering and GO Term Enrichment with stem: updated stem analysis)

     

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(cur | prev) . . (-469). . Leannekuwahara (talk | contribs) (Clustering and GO Term Enrichment with stem: added analysis of prof 48)

     

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(cur | prev) . . (0). . Leannekuwahara (talk | contribs) (Clustering and GO Term Enrichment with stem: editied bullet point)

     

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(cur | prev) . . (-1,475). . Leannekuwahara (talk | contribs) (Clustering and GO Term Enrichment with stem: updated running stem and saving results)

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Subsoontorn Lab:PEOPLE‎‎ (4 changes | history) . . (+11). . [Pakpoom Subsoontorn‎ (4×)]

     

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     07:41  Subsoontorn Lab:Publications‎ (diff | hist) . . (+241). . Pakpoom Subsoontorn (talk | contribs) (Refereed Publications)

16 February 2019

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Leanne Kuwahara-Week 4/5‎‎ (5 changes | history) . . (+20,359). . [Leannekuwahara‎ (5×)]

     

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(cur | prev) . . (+7,245). . Leannekuwahara (talk | contribs) (Protocol: added GRNsight protocol)

     

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(cur | prev) . . (+3,683). . Leannekuwahara (talk | contribs) (Protocol: addedYEASTRACT protocol)

     

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(cur | prev) . . (+9,306). . Leannekuwahara (talk | contribs) (Protocol: added clustering protocol)

     

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(cur | prev) . . (-1). . Leannekuwahara (talk | contribs) (Results: replaced pval chart with zip file)

     

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(cur | prev) . . (+126). . Leannekuwahara (talk | contribs) (Results: added STEM results)

     10:27 (User creation log) . . User account Uncompromised Life (talk | contribs) was created by Yar (talk | contribs) and password was sent by email ‎

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Beauchamp:Publications‎‎ (2 changes | history) . . (+100). . [Michael S Beauchamp‎ (2×)]

     

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(cur | prev) . . (+110). . Michael S Beauchamp (talk | contribs)

     

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     01:10 (Upload log) . . Leannekuwahara (talk | contribs) uploaded File:DGLN3 STEManalysis LK.zip(added STEM figures and tables for significant clusters)

15 February 2019

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BIOL388/S19:Week 4‎‎ (9 changes | history) . . (+236). . [Kam D. Dahlquist‎ (9×)]

     

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(cur | prev) . . (+202). . Kam D. Dahlquist (talk | contribs) (Summary of what you need to turn in for the individual Weeks 4 and 5 assignments: added info for files to submit for week 5)

     

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(cur | prev) . . (+424). . Kam D. Dahlquist (talk | contribs) (Visualizing Your Gene Regulatory Networks with GRNsight (Tuesday, Feb. 21): notes about floating nodes)

     

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(cur | prev) . . (+3). . Kam D. Dahlquist (talk | contribs) (Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes (Tuesday, Feb. 19): increased range to 15-20)

     

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(cur | prev) . . (+11). . Kam D. Dahlquist (talk | contribs) (Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes (Tuesday, Feb. 19): added ZAP1)

     

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(cur | prev) . . (+2). . Kam D. Dahlquist (talk | contribs) (Clustering and GO Term Enrichment with stem (part 2): changed "final" to "research" presentation)

     

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(cur | prev) . . (-26). . Kam D. Dahlquist (talk | contribs) (Clustering and GO Term Enrichment with stem (part 2): revised search instructions)

     

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(cur | prev) . . (+57). . Kam D. Dahlquist (talk | contribs) (Clustering and GO Term Enrichment with stem (part 2): link to go-obo files)

     

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(cur | prev) . . (+56). . Kam D. Dahlquist (talk | contribs) (Clustering and GO Term Enrichment with stem (part 2): link to associations file)

     

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(cur | prev) . . (-493). . Kam D. Dahlquist (talk | contribs) (Clustering and GO Term Enrichment with stem (part 2): change instructions to deal with annotation file issue)

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Beauchamp:Publications‎‎ (3 changes | history) . . (+76). . [Michael S Beauchamp‎ (3×)]

     

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(cur | prev) . . (+13). . Michael S Beauchamp (talk | contribs)

     

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(cur | prev) . . (+22). . Michael S Beauchamp (talk | contribs)

     

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(cur | prev) . . (+41). . Michael S Beauchamp (talk | contribs)


  • See this page for a draft implementation.
  • See this page for a draft on model implementations following CellML 1.1.