Sep. 24 2010
Niklas, Paul, Paresh, Kristian, Fabian
- Do we need all of the three Requirements for a gold medal or just one of these? -> E-Mail to the HQ
- Collaboration -> The things we have done are not enough. We could implement a converter for Geneious <->BioBrick™ formate. An other idea was to write a program that helps the Labteam to design primer.
- Niklas showed us his Blast-Search-Robot. It works good. One question was the menu button position.
- Paresh made a translation-Robot. The six-reading-frame still a problem.
- But now they can upload to sourceforge.
- For the Human practise we could write a Safety-Test-Robot witch looks for virus information in the sequence.
- For donation: Niklas have a contact person at SAP. We will write a letter, maybe we get some money.
- More function in the wave:
- BioBrick import and export with the option to choose/search a Part by No.
- The same for other Databases e.g. Genbank
- seaching for restriction-sites
Sep. 27 2010
Niklas, Paresh, Fabian
- Spoke about the conversation Fabian and Paul had with Kristian
- Fabian showed some new ideas for robots and explained the biology behind them.
- Primer design
- Colored DNA tripplet
- Database download
- Virus check
Paresh had the idea for a Umbrella-robot. It lists all the available robots and lets them add in the wave. We meet Fr. 1.oct. 7pm at bio II/III
Sep. 30 2010
Niklas, Paresh, Fabian, Volker (LabTeam)
- Volker explained us the rules for primers design.
- The Translation Robot and the Blast Robot are fixed. There are a new local alignment Robot (Niklas)
- Kristian is not here tomorrow so we will write him an e-mail to show him the new Robots.
Oct. 5 2010
Fabian showed Kristian the new robots and discussed the functionality and the usability.
- Translation Robot (firstname.lastname@example.org)
- The view should be something like 1. original DNA-Strand 2. first Frame (with all proteins) a.s.o. and all among each other.
- -M--E--F--S--L--*------------M--E--F--S--L--*- (look for the right positions in the edit window)
- In the input matrix there should be an option to choose the start/stop codons and something to choose the organism.
- Primer Design Robot (email@example.com)
- An option to choose the add-on-tail (iGEM standard, own sequence, none)
- Maybe we could implement two different versions to calculate the temperature.
- Restriction Enzymes Robot (REBase)
- Enzymes from the workspace (could be more than 50 to select like the sequences). or something to type it like this: EcoRI, XbaI, ... . One selection for iGEM.
- min and max cut (the length the enzymes will cut)
- EcoRI: Start: 10, 55, 126, ... XbaI: Start: 26, 71, 99, ... view like this: EcoRI | XbaI |
- GCATGCGCTAGCTGCTGAGCATGAATTCACTGTTCTAGAATCGTACT (look for the right positions in the edit window)
- Alignment Robot (firstname.lastname@example.org)
- Show the algorithm which is used (niedelman/wunsch...smith waterman...).
- Blast Robot
- restart the BlastRobot Project
Is it possible to scroll the menu with the wave?
3rd wave for graphics like the workspace.
Oct. 7 2010
Fabian, Kristian, Niklas
We discussed some (new) Ideas we could implement:
- Ligate Bioprick parts
- Import of GenBank etc is important
- Display features (annotations)
- Is it possible to work with selected Sequences in the main Wave?
Keep 5' -> 3' direction!
Okt. 11 2010
Niklas, Fabian, Paresh
- Annotation robot: how to display the output. We will try using the GadgetView Gadget and adjust it to display annotations.
- Translation Robot output now looks good. A problem is, that Biojava translate seems to take long. Maybe write own translation method?
- Talked about the organism identifier robot. Checked codon usage database.
Oct. 12 2010
Jörg, Paresh, Fabian, Niklas
- Paresh presented the latest version of Translation Robot which works well. we will move the coloring form the robots to the gadget to gain performance
- Niklas presented the PartsRegistry import function which got included in the main robot.
- We created a new synbiowave-V2-001.jar as the new developer library.
- Next meeting: Oct. 14 @Lab(Kitchen)
Oct. 15 2010
Paresh, Fabian, Niklas
We created a "roadmap" of all the tasks that we still have to do and assigned each of them to one of us
- Home (Fabian)
- Team (Fabian)
- Project (Paresh) (Summary)
- User (Niklas)
- User Guide (Niklas) (Requirements)
- The Robots (Paresh, Niklas)
- Developer (Niklas)
- Code (Niklas)
- Technologies (Niklas) (Wave, BioJava, ...)
- Architecture (Paresh)
- Availability (Paresh)
- Notebook (Fabian)(aka lab journal)
- Human Practise (Niklas)
- finish existing robots (Paresh, Niklas)
- Blast search robot (Niklas)
- "likelihood" robot (Paresh)
- Genbank, EMBL import (Niklas)
- Deadline: Oct. 24 (meeting TBA)
Oct. 21 2010
Fabian, Paresh, Jörg, Niklas
- We discussed some details of the wiki (pictures, ect.)
- Worked together on the new circular view
- Tried the new Wave-in-a-box -> The client is still in beta stage and its not sure if robots will work, so no alternative for the jamboree.
Oct. 22- 24 2010
Fabian, Paresh, Niklas
- Wrote the wiki together
Oct. 25 2010
Fabian, Jörg, Niklas
- We created the new wave window for graphics