Difference between revisions of "Registry of Standard Biological Models"

From OpenWetWare
Jump to: navigation, search
 
(2 intermediate revisions by the same user not shown)
Line 10: Line 10:
 
|colspan=2 width="705px" class="blue"|
 
|colspan=2 width="705px" class="blue"|
 
{|width="95%" class="blue" align="center" style="border:0px" cellspacing="0"
 
{|width="95%" class="blue" align="center" style="border:0px" cellspacing="0"
|align="center"|'''Talk to us at''' - [[BioSysBio:abstracts/2007/Vincent_Rouilly | '''BioSysBio 2007''']], [[Registry of Standard Biological Models/Presentation | '''iGEM Jamboree Workshop 2007''']]  
+
|align="center"|'''Talk to us at''' - [[BioSysBio:abstracts/2007/Vincent_Rouilly | '''BioSysBio 2007''']], [http://www.syntheticbiology.ethz.ch/conf_2007 SB3.0], and [[Registry of Standard Biological Models/Presentation | '''iGEM Jamboree Workshop 2007''']]  
 
|}
 
|}
 
|-
 
|-
Line 25: Line 25:
 
{|width="95%" class="blue" align="center" valign="top" style="border:0px" cellspacing="0"
 
{|width="95%" class="blue" align="center" valign="top" style="border:0px" cellspacing="0"
 
|'''Activities'''
 
|'''Activities'''
*[[/Registry organization|Planning]] the architecture of a registry of Standard Biological Models.
+
*[[/Registry organization|Planning]] the architecture of a registry of standard biological models.
 
*Building a [[Registry of Standard Biological Models/Model Catalog|collection]] of standard biological models.
 
*Building a [[Registry of Standard Biological Models/Model Catalog|collection]] of standard biological models.
 
*Define a modeling description language that is:
 
*Define a modeling description language that is:
**Machine readable (XML, RDF)
+
**Machine readable
 
**Capable of describing gene expression networks
 
**Capable of describing gene expression networks
 
**Modular (standardized defined inputs/ouputs)
 
**Modular (standardized defined inputs/ouputs)

Latest revision as of 14:49, 4 October 2007

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:

26 September 2017

     09:21 

(User creation log). .

[Yar‎ (3×)]

     

09:21

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

     

09:21

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

     

09:03

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

N    09:13 

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

     

09:13

(cur | prev) . . (+23). . Merman (talk | contribs) (test link)

N    

09:09

(cur | prev) . . (+9). . Merman (talk | contribs) (testing no captcha)

     08:42 

Hoatlin:BMB seminar series 2017-2018‎‎ (2 changes | history) . . (+24). . [Maureen E. Hoatlin‎ (2×)]

     

08:42

(cur | prev) . . (-75). . Maureen E. Hoatlin (talk | contribs) (Seminar Schedule 2017-2018)

     

08:41

(cur | prev) . . (+99). . Maureen E. Hoatlin (talk | contribs) (Seminar Schedule 2017-2018)

     07:32 

Tomlinson:News‎‎ (2 changes | history) . . (+83). . [Ryan E. Tomlinson‎ (2×)]

     

07:32

(cur | prev) . . (+11). . Ryan E. Tomlinson (talk | contribs) (2017)

     

07:32

(cur | prev) . . (+72). . Ryan E. Tomlinson (talk | contribs)

     07:30 

Tomlinson:Lab Members‎‎ (3 changes | history) . . (+46). . [Ryan E. Tomlinson‎ (3×)]

     

07:30

(cur | prev) . . (+4). . Ryan E. Tomlinson (talk | contribs) (Kimberly Huang)

     

07:30

(cur | prev) . . (+4). . Ryan E. Tomlinson (talk | contribs) (Emily Rumpf)

     

07:30

(cur | prev) . . (+38). . Ryan E. Tomlinson (talk | contribs)

     07:11 (Move log) . . Karmella Haynes (talk | contribs) moved page BME100 f2017:Group6 W1030 L6 to BME100 f2017:Group6 W1030 L6 delete this page(Class assignment. Students did not follow instructions for generating a page with correct formatting. Freeing up the page title to allow students to re-generate the correct page.)
     07:07  BME100 f2017:Projects6‎ (diff | hist) . . (+19). . Karmella Haynes (talk | contribs)
     07:07  BME100 f2017:Projects5‎ (diff | hist) . . (+19). . Karmella Haynes (talk | contribs)
     07:07  BME100 f2017:Projects4‎ (diff | hist) . . (+19). . Karmella Haynes (talk | contribs)
     07:01  BME100 f2017:Projects3‎ (diff | hist) . . (+19). . Karmella Haynes (talk | contribs)
     06:59  BME100 f2017:Projects2‎ (diff | hist) . . (+19). . Karmella Haynes (talk | contribs)

     04:06 

Butlin:Unix for Bioinformatics - advanced tutorial‎‎ (3 changes | history) . . (+334). . [Claudius E Kerth‎ (3×)]

     

04:06

(cur | prev) . . (+148). . Claudius E Kerth (talk | contribs) (Added troublehooting tip: when rename.pl download link does not work, go to my Dropbox)

     

02:44

(cur | prev) . . (+168). . Claudius E Kerth (talk | contribs) (added Troubleshooting tip)

 m   

02:36

(cur | prev) . . (+18). . Claudius E Kerth (talk | contribs) (TASK 5: I have split my reads by barcode and I have quality filtered them. Now I want to know how many reads I have left from each (barcoded) individual. How can I find that out?)

25 September 2017

     21:19 

BME100 f2017:Group12 W0800 L3‎‎ (12 changes | history) . . (+3,361). . [Priscilla Y. Han‎ (12×)]

     

21:19

(cur | prev) . . (+25). . Priscilla Y. Han (talk | contribs) (Descriptive Stats and Graph)

     

21:15

(cur | prev) . . (+70). . Priscilla Y. Han (talk | contribs) (Descriptive Stats and Graph)

     

21:11

(cur | prev) . . (-3). . Priscilla Y. Han (talk | contribs) (Experimental Design of Device)

     

21:10

(cur | prev) . . (-12). . Priscilla Y. Han (talk | contribs) (Experimental Design of Device)

     

21:10

(cur | prev) . . (+15). . Priscilla Y. Han (talk | contribs) (Experimental Design of Device)

     

21:09

(cur | prev) . . (+3,181). . Priscilla Y. Han (talk | contribs) (Experimental Design of Device)

     

21:05

(cur | prev) . . (+5). . Priscilla Y. Han (talk | contribs) (Descriptive Stats and Graph)

     

21:03

(cur | prev) . . (+25). . Priscilla Y. Han (talk | contribs) (Descriptive Stats and Graph)

     

21:01

(cur | prev) . . (+2). . Priscilla Y. Han (talk | contribs) (Descriptive Stats and Graph)

     

20:58

(cur | prev) . . (+29). . Priscilla Y. Han (talk | contribs) (Descriptive Stats and Graph)

     

20:57

(cur | prev) . . (-3). . Priscilla Y. Han (talk | contribs) (Descriptive Stats and Graph)

     

20:55

(cur | prev) . . (+27). . Priscilla Y. Han (talk | contribs) (Descriptive Stats and Graph)

     21:19 

(Upload log). .

[Priscilla Y. Han‎ (7×)]

     

21:19

. . Priscilla Y. Han (talk | contribs) uploaded File:Pulsingbargraph12.png

     

21:18

. . Priscilla Y. Han (talk | contribs) uploaded File:Mypear sonheart12.png

     

21:18

. . Priscilla Y. Han (talk | contribs) uploaded File:Heartratespree12.png

     

21:04

. . Priscilla Y. Han (talk | contribs) uploaded File:Scrnshotspree12.png

     

20:59

. . Priscilla Y. Han (talk | contribs) uploaded File:2columnbarsspree.png

     

20:56

. . Priscilla Y. Han (talk | contribs) uploaded a new version of File:Mypear sonr.png

     

20:56

. . Priscilla Y. Han (talk | contribs) uploaded File:Mypear sonr.png

     20:33 

BME100 f2017:Group8 W1030 L3‎‎ (9 changes | history) . . (+501). . [Jennifer L. Brodsky‎ (9×)]

     

20:33

(cur | prev) . . (+5). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     

20:32

(cur | prev) . . (+112). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     

20:29

(cur | prev) . . (0). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     

20:28

(cur | prev) . . (+13). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     

20:28

(cur | prev) . . (-1). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     

20:26

(cur | prev) . . (+1). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     

20:26

(cur | prev) . . (+177). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     

20:25

(cur | prev) . . (+7). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     

20:24

(cur | prev) . . (+187). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

N    20:17  BME100 f2017:Group10 W0800 L3‎ (diff | hist) . . (+767). . Whitney Hirano (talk | contribs) (Created page with "5. The mean value of heart rate calculated from the pulse ox was 98.3673 beats/min with a standard deviation of 22.2273, while the mean value of heart rate calculated from the...")

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