Registry of Standard Biological Models

From OpenWetWare
Jump to: navigation, search
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:

18 April 2018

     20:43 

X-Lab‎‎ (4 changes | history) . . (0). . [ChanEngr‎ (4×)]

     

20:43

(cur | prev) . . (0). . ChanEngr (talk | contribs)

     

20:38

(cur | prev) . . (0). . ChanEngr (talk | contribs)

     

20:36

(cur | prev) . . (0). . ChanEngr (talk | contribs)

     

20:35

(cur | prev) . . (0). . ChanEngr (talk | contribs)

 m   16:47 

User:Korey Griffin‎‎ (2 changes | history) . . (+32). . [Korey Griffin‎ (2×)]

 m   

16:47

(cur | prev) . . (-47). . Korey Griffin (talk | contribs) (Contact)

 m   

11:03

(cur | prev) . . (+79). . Korey Griffin (talk | contribs) (Empirical Resources)

     15:21 

User:Johannes Stuttmann‎‎ (3 changes | history) . . (+4,407). . [Johannes Stuttmann‎ (3×)]

     

15:21

(cur | prev) . . (+1,692). . Johannes Stuttmann (talk | contribs)

     

14:42

(cur | prev) . . (+2,470). . Johannes Stuttmann (talk | contribs)

     

13:09

(cur | prev) . . (+245). . Johannes Stuttmann (talk | contribs)

     13:02  Hydrochloric acid‎ (diff | hist) . . (+1). . Yar (talk | contribs) (typing error from user email)

     12:52 

(User creation log). .

[Yar‎ (2×)]

     

12:52

. . User account Ally B (talk | contribs) was created by Yar (talk | contribs) and password was sent by email ‎

     

12:52

. . User account Jakob (talk | contribs) was created by Yar (talk | contribs) and password was sent by email ‎

N    12:46 

BIOL478/S18:Microarray Data Analysis‎‎ (24 changes | history) . . (+34,776). . [Kam D. Dahlquist‎ (24×)]

     

12:46

(cur | prev) . . (-70). . Kam D. Dahlquist (talk | contribs) (Gridding and Generating Intensity Data: remove old Brightspace link)

     

12:45

(cur | prev) . . (+1). . Kam D. Dahlquist (talk | contribs) (GenePix Pro Protocol (Steps 1-3): fix Brightspace link to raw data)

     

12:16

(cur | prev) . . (+1,241). . Kam D. Dahlquist (talk | contribs) (Before We Begin: add section on lab notebook)

     

12:04

(cur | prev) . . (0). . Kam D. Dahlquist (talk | contribs) (Background: fix list formatting)

     

12:03

(cur | prev) . . (+108). . Kam D. Dahlquist (talk | contribs) (Background: add GRNsight)

     

12:02

(cur | prev) . . (+3,845). . Kam D. Dahlquist (talk | contribs) (Identifying regulatory transcription factors responsible for observed changes in gene expression (step 10): paste in GRNsight instructions)

     

12:00

(cur | prev) . . (+3,072). . Kam D. Dahlquist (talk | contribs) (Identifying regulatory transcription factors responsible for observed changes in gene expression (step 10): paste in protocol from Biomath modeling, modify for HMO1)

     

11:56

(cur | prev) . . (+114). . Kam D. Dahlquist (talk | contribs) (Clustering and GO Term Enrichment with stem (steps 7-8): add section for step 10)

     

11:55

(cur | prev) . . (-751). . Kam D. Dahlquist (talk | contribs) (Clustering and GO Term Enrichment with stem (steps 7-8): delete comment, emphasize to unzip)

     

11:52

(cur | prev) . . (0). . Kam D. Dahlquist (talk | contribs) (Modified t test for each timepoint: fix formula)

     

11:29

(cur | prev) . . (+52). . Kam D. Dahlquist (talk | contribs) (Sanity Check: Number of genes significantly changed: add label to link)

     

11:29

(cur | prev) . . (+29). . Kam D. Dahlquist (talk | contribs) (Sanity Check: Number of genes significantly changed: add link to xkcd comic)

     

11:25

(cur | prev) . . (-360). . Kam D. Dahlquist (talk | contribs) (replace opi1 with hmo1)

     

11:24

(cur | prev) . . (+18). . Kam D. Dahlquist (talk | contribs) (replace wt with dHMO1)

     

11:22

(cur | prev) . . (+36). . Kam D. Dahlquist (talk | contribs) (Modified t test for each timepoint: replace wt with dHMO1)

     

11:20

(cur | prev) . . (-22). . Kam D. Dahlquist (talk | contribs) (Looking at the raw data: fix links to SGD)

     

11:18

(cur | prev) . . (+3). . Kam D. Dahlquist (talk | contribs) (Downloading the Data: change to hmo1)

     

11:07

(cur | prev) . . (+35). . Kam D. Dahlquist (talk | contribs) (Statistical Analysis (Step 6): change to delta-hmo1)

     

10:35

(cur | prev) . . (+61). . Kam D. Dahlquist (talk | contribs) (GenePix Pro Protocol (Steps 1-3): note that this will be demo'd, change opi1 to hmo1)

     

10:33

(cur | prev) . . (+27). . Kam D. Dahlquist (talk | contribs) (Background: steps 1-3 done for you)

     

10:32

(cur | prev) . . (+74). . Kam D. Dahlquist (talk | contribs) (Background: add link for YEASTRACT)

     

10:30

(cur | prev) . . (+15). . Kam D. Dahlquist (talk | contribs) (change dates, mention of Windows 10)

     

10:26

(cur | prev) . . (+27,230). . Kam D. Dahlquist (talk | contribs) (paste in from S18)

N    

10:26

(cur | prev) . . (+18). . Kam D. Dahlquist (talk | contribs) (create page with under construction flag)

     10:27  Dahlquist:Protocols‎ (diff | hist) . . (+152). . Kam D. Dahlquist (talk | contribs) (Dry Lab Protocols: create link to BIOL 478 Spring 2018 protocol)

     09:43 

Crosby:Lab Members‎‎ (2 changes | history) . . (+41). . [Mohammad H. Dezfulian‎ (2×)]

     

09:43

(cur | prev) . . (+71). . Mohammad H. Dezfulian (talk | contribs) (Recent Alumni)

     

09:41

(cur | prev) . . (-30). . Mohammad H. Dezfulian (talk | contribs) (Graduate Students)

     08:35  CAMRI:SeminarSeries‎ (diff | hist) . . (+62). . Lexi E. Crommett (talk | contribs)
     08:00 (Upload log) . . Reinca (talk | contribs) uploaded File:FinalView2.JPG
     01:58  User:Timothee Flutre‎ (diff | hist) . . (+141). . Timothee Flutre (talk | contribs) (Links: add open data repos)

17 April 2018

     23:41  BME100 s2018:Group7 W1030 L6‎ (diff | hist) . . (+454). . Dragos (talk | contribs) (Intro to Computer-Aided Design)

     23:23 

BME100 s2018:Group8 W0800 L6‎‎ (3 changes | history) . . (+601). . [Leaverjill‎ (3×)]

     

23:23

(cur | prev) . . (+293). . Leaverjill (talk | contribs) (Feature 2: Hardware - PCR Machine & Fluorimeter)

     

23:20

(cur | prev) . . (+1). . Leaverjill (talk | contribs) (Bayesian Statistics)

     

23:19

(cur | prev) . . (+307). . Leaverjill (talk | contribs) (Feature 2: Hardware - PCR Machine & Fluorimeter)

     23:22  BME100 s2018:Group1 W1030 L6‎ (diff | hist) . . (+8). . Erik Halsband (talk | contribs) (Intro to Computer-Aided Design)
     23:18 (Upload log) . . Erik Halsband (talk | contribs) uploaded a new version of File:ClosedFlourimeter.JPG(Re-rendered with updated walls.)

     23:17 

BME100 s2018:Group1 W0800 L6‎‎ (2 changes | history) . . (+4). . [Yaroomba‎ (2×)]

     

23:17

(cur | prev) . . (+2). . Yaroomba (talk | contribs) (Feature 2)

     

23:17

(cur | prev) . . (+2). . Yaroomba (talk | contribs) (Feature 1)


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