Difference between revisions of "Endy:Notebook/Wetware IDE"

From OpenWetWare
Jump to: navigation, search
(BioBrick Studio Source Code)
(Project Description)
Line 14: Line 14:
 
|colspan="2"|
 
|colspan="2"|
 
==Project Description==
 
==Project Description==
*We are interested in an integrated development environment (IDE) that supports review, design, and implemention of standard biological parts
+
*We are in pursuit of an integrated development environment (IDE) that supports review, design, and implemention of standard biological parts
 
*Our core goals are to develop programming languages, information models, communication/computational architectures that support the development and responsible use of standard biological parts.
 
*Our core goals are to develop programming languages, information models, communication/computational architectures that support the development and responsible use of standard biological parts.
  

Revision as of 14:53, 9 March 2010

<!-- sibboleth --><div id="lncal1" style="border:0px;"><div style="display:none;" id="id">lncal1</div><div style="display:none;" id="dtext"></div><div style="display:none;" id="page">Endy:Notebook/Wetware IDE</div><div style="display:none;" id="fmt">yyyy/MM/dd</div><div style="display:none;" id="css">OWWNB</div><div style="display:none;" id="month"></div><div style="display:none;" id="year"></div><div style="display:none;" id="readonly">Y</div></div>

Owwnotebook icon.png <sitesearch>title=Search this Project</sitesearch>

Customize your entry pages <html><img src="/images/a/aa/Help.png" border="0" /></html>

Project Description

  • We are in pursuit of an integrated development environment (IDE) that supports review, design, and implemention of standard biological parts
  • Our core goals are to develop programming languages, information models, communication/computational architectures that support the development and responsible use of standard biological parts.

Review

Existing Software Tools

Peer-Reviewed Literature

  • Czar MJ, et al. Gene synthesis demystified. Trends in Biotechnology 27(2):63-72. (2009) Link
  • Goler JA, et al. Genetic design: rising above the sequence. Trends in Biotechnology 26(10):538-44. (2008) Link
  • Peccoud J, et al. Targeted development of registries of biological parts PLoS ONE 3(7):e2671. (2008) Link
  • Cai, et al. A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23(20): 2760-2767. (2007) Link
  • Villalobos, et al. Gene Designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics 2006 7:285. Link

Use Cases, Requirements, Comments

Primary requirements: Physical building of standard biological parts.

  • primers design for part cloning (including prefix and suffix. see:Ginkgo)
  • primers design for mutagenize the restriction sites present in the original sequence to fit to the BBS designed one. A very good program here: stratagene


Click here to read the ongoing discussions... You are highly encouraged to contribute!

Design

General

  • Use a studio motif
    • Foyer - Entry point for the application
    • Library - Area to study natural or non-standard DNA sequences, basic and composite parts
    • Palette - Developers personal collection of DNA sequences, basic and composite parts
    • Canvas - Design environment DNA sequence refinement, basic and composite part development
    • Services - Area to explore the availability and cost of implementation services

Icons for BioBrick Studio iPhone

DNA Sequence Refinement Notebook

Implementation

Source Code

SynBioLib

Maintenance

Notes


Recent changes

19 October 2017

     15:43  User:Julie A. Fogarty‎ (diff | hist) . . (+46). . Julie A. Fogarty (talk | contribs) (Julie A. Fogarty)

     15:33 

Rich Lab:Funding‎‎ (2 changes | history) . . (-12). . [Isabel C. Morales‎ (2×)]

     

15:33

(cur | prev) . . (+12). . Isabel C. Morales (talk | contribs)

     

14:06

(cur | prev) . . (-24). . Isabel C. Morales (talk | contribs)

     14:58 

CONJ606:Materials‎‎ (2 changes | history) . . (+1,004). . [Weinjule‎; Peteral‎]

     

14:58

(cur | prev) . . (+685). . Peteral (talk | contribs) (Week 2: Me Myself and I-dentifiers, The Key To Immortality (Persistence))

     

12:15

(cur | prev) . . (+319). . Weinjule (talk | contribs) (Papers)

     14:52 

User:Peteral‎‎ (3 changes | history) . . (+1,264). . [Peteral‎ (3×)]

     

14:52

(cur | prev) . . (+185). . Peteral (talk | contribs) (Alec's Discussion Questions)

     

13:52

(cur | prev) . . (+351). . Peteral (talk | contribs) (Alec's Discussion Questions)

     

10:53

(cur | prev) . . (+728). . Peteral (talk | contribs) (Alec's Discussion Questions)

     14:13 

BME100 f2017:Group14 W0800 L4‎‎ (9 changes | history) . . (+9). . [Shae M. Diaz‎ (9×)]

     

14:13

(cur | prev) . . (+8). . Shae M. Diaz (talk | contribs) (Protocol)

     

14:12

(cur | prev) . . (-31). . Shae M. Diaz (talk | contribs) (TEAM MEMBERS)

     

14:10

(cur | prev) . . (+31). . Shae M. Diaz (talk | contribs) (TEAM MEMBERS)

     

14:09

(cur | prev) . . (+4). . Shae M. Diaz (talk | contribs) (TEAM MEMBERS)

     

14:05

(cur | prev) . . (-1). . Shae M. Diaz (talk | contribs) (TEAM MEMBERS)

     

14:05

(cur | prev) . . (+1). . Shae M. Diaz (talk | contribs) (TEAM MEMBERS)

     

14:04

(cur | prev) . . (-1). . Shae M. Diaz (talk | contribs) (TEAM MEMBERS)

     

13:55

(cur | prev) . . (+1). . Shae M. Diaz (talk | contribs) (TEAM MEMBERS)

     

13:55

(cur | prev) . . (-3). . Shae M. Diaz (talk | contribs) (TEAM MEMBERS)

 m   14:12  Swartz‎ (diff | hist) . . (+61). . Marcus Rohovie (talk | contribs)
     14:10 (Move log) . . Marcus Rohovie (talk | contribs) moved page Swartz to Swartz:Main

     14:08 

(Upload log). .

[Thorntca‎; Shae M. Diaz‎ (3×)]

     

14:08

. . Shae M. Diaz (talk | contribs) uploaded File:100profileshae.JPG

     

14:01

. . Shae M. Diaz (talk | contribs) uploaded File:Shaediaz100.JPG

     

13:51

. . Shae M. Diaz (talk | contribs) uploaded File:BME100ShaeD.JPG

     

13:17

. . Thorntca (talk | contribs) uploaded File:2Dgel.png.jpg

     13:52 

Klenow Assembly Method: Seamless cloning‎‎ (3 changes | history) . . (+101). . [David M.D. Bailey‎ (3×)]

     

13:52

(cur | prev) . . (-5). . David M.D. Bailey (talk | contribs) (The Klenow Assembly Method (KAM) for the seamless cloning of overlapping double stranded DNA fragments: Very cheap alternative to the Gibson Assembly)

     

13:51

(cur | prev) . . (+1). . David M.D. Bailey (talk | contribs) (The Klenow Assembly Method (KAM) for the seamless cloning of overlapping double stranded DNA fragments: Very cheap alternative to the Gibson Assembly)

     

13:50

(cur | prev) . . (+105). . David M.D. Bailey (talk | contribs) (The Klenow Assembly Method (KAM) for the seamless cloning of overlapping double stranded DNA fragments: Very cheap alternative to the Gibson Assembly)

     13:22 

User:Thorntca‎‎ (8 changes | history) . . (+529). . [Thorntca‎ (8×)]

     

13:22

(cur | prev) . . (+145). . Thorntca (talk | contribs)

     

13:19

(cur | prev) . . (+17). . Thorntca (talk | contribs)

     

13:19

(cur | prev) . . (+4). . Thorntca (talk | contribs)

     

13:18

(cur | prev) . . (+30). . Thorntca (talk | contribs)

     

13:16

(cur | prev) . . (+417). . Thorntca (talk | contribs)

     

12:52

(cur | prev) . . (+12). . Thorntca (talk | contribs)

     

12:51

(cur | prev) . . (-5). . Thorntca (talk | contribs)

     

12:51

(cur | prev) . . (-91). . Thorntca (talk | contribs)

     12:27 

User:Madeline.churchill‎‎ (2 changes | history) . . (+302). . [Madeline.churchill‎ (2×)]

     

12:27

(cur | prev) . . (0). . Madeline.churchill (talk | contribs) (TZAP protein controls telomere Trimming process)

     

12:27

(cur | prev) . . (+302). . Madeline.churchill (talk | contribs) (Madeline Churchill's Discussion Page)

     09:17  BioMicroCenter:BIG meeting‎ (diff | hist) . . (+19). . George W Bell (talk | contribs) (2017-2018 academic year)
     07:06 (User creation log) . . User account Newfish (talk | contribs) was created by Yar (talk | contribs) and password was sent by email ‎

     04:10 

BioMicroCenter:BioinfoClasses‎‎ (3 changes | history) . . (+132). . [Charlie Whittaker‎ (3×)]

     

04:10

(cur | prev) . . (+9). . Charlie Whittaker (talk | contribs) (Teaching Schedule)

     

04:09

(cur | prev) . . (0). . Charlie Whittaker (talk | contribs) (Teaching Schedule)

     

04:08

(cur | prev) . . (+123). . Charlie Whittaker (talk | contribs) (Teaching Schedule)

     03:36  User:Timothee Flutre‎ (diff | hist) . . (+146). . Timothee Flutre (talk | contribs) (add contrib breedR and SO)

 m   02:27 

How to write a research paper‎‎ (2 changes | history) . . (+91). . [Formand‎ (2×)]

 m   

02:27

(cur | prev) . . (-1). . Formand (talk | contribs) (External links)

 m   

02:24

(cur | prev) . . (+92). . Formand (talk | contribs) (External links)

18 October 2017

     19:09  BME100 f2017:Group10 W0800 L4‎ (diff | hist) . . (+1). . Osvaldo J Pagan (talk | contribs)
     15:56  BME100 f2017:Group8 W1030 L4‎ (diff | hist) . . (+409). . Jennifer L. Brodsky (talk | contribs) (Research and Development)
     15:20  BME100 f2017:Group7 W0800 L4‎ (diff | hist) . . (-4). . Miguel R. Almanza Lopez (talk | contribs) (OUR TEAM)
     15:16 (Upload log) . . Miguel R. Almanza Lopez (talk | contribs) uploaded File:MralPoopy.jpg

     14:40 

BME100 f2017:Group1 W1030 L4‎‎ (2 changes | history) . . (+61). . [Abby E. Krell‎ (2×)]

     

14:40

(cur | prev) . . (+33). . Abby E. Krell (talk | contribs) (Protocol)

     

14:39

(cur | prev) . . (+28). . Abby E. Krell (talk | contribs) (Protocol)