Team:Heidelberg/Notebook modeling
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** Discuss general ideas of our Database Structure and Content | ** Discuss general ideas of our Database Structure and Content | ||
** An introduction into PromoterSweep (LINK). PromoterSweep screens a given sequence for conserved regions giving us consensus sequences and moreover screens them for TFBS by using database search (TRANSFAC, Jasper) (LINK) | ** An introduction into PromoterSweep (LINK). PromoterSweep screens a given sequence for conserved regions giving us consensus sequences and moreover screens them for TFBS by using database search (TRANSFAC, Jasper) (LINK) | ||
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** Our new database should contain following informations: promoter sequence, TFs, TFBS, position of TFBS, number of binding TFBS, "host organism" | ** Our new database should contain following informations: promoter sequence, TFs, TFBS, position of TFBS, number of binding TFBS, "host organism" | ||
** We decide to choose MySQL as a appropiate language solving this challenge which allows us also a graphical representation of the database on the web later. | ** We decide to choose MySQL as a appropiate language solving this challenge which allows us also a graphical representation of the database on the web later. | ||
** GUI on wiki: which language? php? javascript? | ** GUI on wiki: which language? php? javascript? | ||
** Problems: access to PromoterSweep (Husar Bioinformatics Group, DKFZ), choice of Promoter Database (DoOP, UCSC, EnsEMBL) (LINK) | ** Problems: access to PromoterSweep (Husar Bioinformatics Group, DKFZ), choice of Promoter Database (DoOP, UCSC, EnsEMBL) (LINK) | ||
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+ | * aim: create database until end of August | ||
== 8-3-2009 == | == 8-3-2009 == |
Revision as of 22:42, 18 October 2009
Notebook HEARTBEATWelcome to the notebook of the HEARTBEAT (Heidelberg Artificial Transcription Factor Binding Sites Assembly and Engineering Tool) project. This notebook comprises the work on three sublanes: HEARTBEAT database (DB), HEARTBEAT graphical user interface (GUI) and HEARTBEAT fuzzy modeling (FN) as well as some additional work on logo as well as wiki design. Have fun!
Contents
7-27-2009
8-3-2009
8-4-2009
8-5-2009
8-6-2009
8-7-2009
8-12-2009
8-14-2009
8-17-2009
8-18-2009
- Digested p31 and a Jet insert with NheI and SpeI. -Ligated both together for 3 hrs at RT. (insert:vector= 1:1, 3:1, 1:3) -Transformed bacteria with ligate and plated them on Amp plates. -Repeated mutagenesis PCR again for (p33, p35, p37, p37-Ras, p41, p43) 8-19-2009
8-20-2009
8-21-2009
8-22-2009
8-24-2009
8-26-2009BBBing of Insertsequences
8-27-2009
8-28-2009BBBing of Insertsequences2.0
8-29-2009BBBing of Insertsequences2.1
8-31-2009BBBing of Insertsequences2.1 (part 2)
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