Difference between revisions of "Registry of Standard Biological Models"

From OpenWetWare
Jump to: navigation, search
 
(14 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
<div>
 
<div>
{|class="white" cellspacing="3"
+
{|class="white" cellspacing="5" valign="top"
 +
|colspan=2|{{Click || image=RoSBMBanner.png | link=Main_Page| width=705px | height=94px }}
 
|-  
 
|-  
|width="705px" class="blue" colspan=2| {{Registry_of_Standard_Biological_Models/Blurb}}
+
|colspan=2 width="705px" bgcolor="#181860" |
 +
{|width="90%" bgcolor="#181860" align="center" style="border:0px" cellspacing="0"
 +
|bgcolor="#181860"|<font face="tahoma" size="2" color=#ffffff>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.</font>
 +
|}
 
|-
 
|-
 +
|colspan=2 width="705px" class="blue"|
 +
{|width="95%" class="blue" align="center" style="border:0px" cellspacing="0"
 +
|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''']]
 
|}
 
|}
</div>
 
 
{| cellspacing="3"
 
 
|-
 
|-
|colspan=2 width="700px" class="green2"| Talk to us at - [[BioSysBio:abstracts/2007/Vincent_Rouilly | BioSysBio 2007]], [[Registry of Standard Biological Models/Presentation | iGEM Jamboree Workshop]]
+
|width="350px" class="blue" valign="top" |
|-
+
{|width="95%" class="blue" align="center" valign="top" style="border:0px" cellspacing="0"
|width="350px" class="green3" | '''Goals'''
+
|'''Goals'''
 
+
*To contribute to the Open Source [[Synthetic Biology]] effort.
*To contribute to the Open Source Synthetic Biology effort.
+
*To store, curate and support models related to [http://parts.mit.edu physical Biobricks].
*To store, curate and support models related to physical DNA Biobricks.
 
 
*To drive and guide the experimental characterization of BioBricks.
 
*To drive and guide the experimental characterization of BioBricks.
 
*To enable the reuse of modular part models.
 
*To enable the reuse of modular part models.
 
*To provide a forum for modelers to contribute to the BioBricks effort.
 
*To provide a forum for modelers to contribute to the BioBricks effort.
 
+
|}
|width="350px" class="green3" | '''Activities'''
+
|width="350px" class="blue" valign="top" |
 
+
{|width="95%" class="blue" align="center" valign="top" style="border:0px" cellspacing="0"
*Build a 1 to N match between physical DNA parts and models into a database
+
|'''Activities'''
 +
*[[/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.
 
*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)
 
**Hierarchical (models are composable)
 
**Hierarchical (models are composable)
*Capable of describing models that can be related to experimental data.
+
**Capable of describing models that can be related to experimental data.
 +
|}
 +
|-
 +
|}
 +
 
 +
<hr class="divider2">
 +
<div>
 +
 
 +
{|class="white"
 +
|width="700px" class="white" cellpadding="0"|'''Recent edits:'''
 +
|-
 +
|width="700px" class="white" cellpadding="0"|{{Special:Recentchanges/b=Registry_of_Standard_Biological_Models&limit=10}}
 
|-
 
|-
 
|}
 
|}
 +
</div>
 +
<hr class="divider2">
  
 
*See [[Registry of Standard Biological Models/CellML Practical|this page]] for a draft implementation.
 
*See [[Registry of Standard Biological Models/CellML Practical|this page]] for a draft implementation.
 
*See [[Registry_of_Standard_Biological_Models/Basic_Component_Models|this page]] for a draft on model implementations following CellML 1.1.
 
*See [[Registry_of_Standard_Biological_Models/Basic_Component_Models|this page]] for a draft on model implementations following CellML 1.1.
*See [[Registry of Standard Biological Models/General Architecture Discussion|this page]] to access current discussion on the implementation.
 
 
 
= Interesting stuff to explore ... =
 
 
*SBML[http://sbml.org/index.psp] and CellML[http://www.cellml.org/] are already widely used standards. Are they what Synthetic Biology is looking for? 
 
*Petri Nets Markup language is already defining a modular/hierarchical approach. Could be interesting to investigate. [http://www2.informatik.hu-berlin.de/top/pnml/pnml.html]
 
*Standardized outputs: how about using experimental data format to store computed results (like FCS from Flow cytometry), it could help also to define a validation schema when it comes to challenge predicted results with measured ones.
 
 
Original idea
 
 
I'd like to see a centralized and standardized source of models for biological parts and devices.  A good framework for this would be the registry of standard biological parts.  Each part and device should have a simple ODE model of its behavior accompanying it.  In fact, this registry of models would operate identically and confer all the same advantages as a registry of parts.  Namely, it would produce simple standard models of components that could be reliably and rapidly combined to form models of more complex components.  If everybody building models was drawing from the same pool of component models, we could be more sure that those models were an accurate reflection of the physical component.  Again, just as with the registry of physical parts, everytime I wanted to build a model, I wouldn't have to start from scratch, I could start from well-tested components.
 
 
For example a constitutive promoter has a model with no inputs (ignoring polymerase and &sigma; factor levels) and one output, PoPS.  In Matlab, this would be a simple function with no inputs that returns a scalar output which is the PoPS output of the device -
 
 
PoPS_out = R0040;
 
 
A protein generator would have a model with a PoPS input and a protein production rate as output.  For example -
 
 
dP = E0240(PoPS_in);
 
 
Note that E0240 might actually be a collection of part models for an RBS, coding region, and terminator -
 
function dp = E0240(PoPS_in)
 
RiPS = B0032(PoPS_in);
 
translation_rate = E0040(RiPS);
 
dp = B0015(translation_rate);
 
 
 
The part models for R0040 and E0240 could be put together in an obvious way to form a model of a reporter device.
 
 
We already have models for many of our simple parts that could be combined easily if only steady state conditions were considered.  Some more organization would be required to allow each model to represent the time varying behavior of a device as combining devices would require the assembly of ODE's from different files.  It should still be very possible though.
 

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.