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Revision as of 07:22, 29 June 2009

Nina 2 June 2009

Today is the second day of iGEM. Yesterday I spent time looking at java tutorials.

New Tasks Given are to look at tutorials for wiki that will be working or not -- media wiki embedded html for complicated stuff keep clean, so no need to clean up later think of a plug-in 1 wiki entry per week

Nina 3 June 2009

Nina Revko - on UCB campus

My 1st official entry

I am a member of computational team, majoring in bioengineering in fall 2009.

On Monday my team met, and everyone got acquainted with each other. We are still missing one member Lesie, who will join the team on Monday. After meeting with members of computational team, everyone went for a lab safety training and lunch social, where we met other members and leaders including the participants of the wet lab. Instructors were surprised with the size of this year's iGEM team.

Even though, we started working only on Monday, today is Wednesday, and everyone is overwhelmed with tasks and information. I think that we will adjust very soon and will produce effective results.

We got acquainted with Clotho, NetBeans, some Clotho code and CVS already.

This week short-term goals:

search for bugs in Clotho
edit Notebook
modify .html help files

MainToolBar
MySQLlogin

Longer short-term goals:

proof-read and become familiar with the rough draft of paper for assembly of biological parts(implementation of dynamic programming - hash tables in Java - and determining the minimum cost for assembly)
together with Bing, meet with Chris Anderson and Jenn and learn how the robot works in the wet lab + their protocols (.csv file)

Long term goal for the 1st part of iGEM:

Robot/Automation project (brief structure):

select parts (basic and compound)
- do it through Part Manager - 1 click
- put in Algorithm Manager
run Assembly Algorithm w/Algorithm Manager Plug-in => record wells and physical locations of the each part
create 2 protocols (.csv)
1. human
2. robot

both protocols should take into account actions that user should perform (grab samples from freezer with appropriate bar code - talk to wet lab members); the way dilution will be performed; the way plates will be managed before the complete assembly takes place (Plate Manager)

--NinaRevko 23:05, 3 June 2009 (UTC)

Nina 5 June 2009

After meeting with J.Christopher Anderson... The questions raised:

how to delete theoretical parts from the database (with no associated physical part?
requirements that will be tried to be implemented with the following assumptions:
- start with a single plate where the basic parts are located - are all in 1 plate put there by user
- cell stocks are not taken into account initially
- bring parts in/out - allow for flexibility and playing around with parts
- export assembly tree into a .csv file for robot with taking into account of "left-y", "right-y" and different antibiotics compatibility (AC, CA, AK, KA, CK, KC) - "lefty"/"righty" are currently not specified in db
- after the robot is done and parts were made, display what parts were successful -- allow for user's input (in form of a tree?!)

Nina 10 June 2009

Yesterday I made my first sample plugin. It was not difficult, but took some time to debug and find out what did not work. The plugIn file name should be "plugin.xml" and it is very important to preserve that format. Yesterday I had another meeting with wet lab representatives discussing the robot protocol. Also I had a chance to take a look at the AssemblyAutomationPlugin on which I will be working in the nearest future. Today Jenn from the wet lab sent the protocol they are using for the robot and I am going through analyzing it right now. Some notes:

min volume for robot - 3ul
max volume for a single 96well plate - 200 ul
max volume for pippetting/mixing for robot???
digest cocktail and lysis mix cannot be done by hand (from Bing)

stock plate (96 well with mini preps)
bigStock plate with H2O, buffer, lysis mix, digest cocktail
dilution plate
reaction plate

Looking at protocol, there should be several blocks done:

running the SDS assembly algorithm, determine the amount of every basic part needed for the building of the final goal part(? what to do about the extra volume of the required reagents? multiply the volume by which factor assuming that some stages need to be re-tried?)
?should we take into account the amount of the stock and prep sep one for each STAGE?
done by user at the present time: making basic parts and miniprep (?put in DB); put in 96 well plate at this time
dilution block (Input--the wells and plate locations of the miniprep and basic parts - if they are in stock plate as specified by the protocol after SDS algo, locations are known); check if the user messed up the plate; the plate with NEB2 Buffer (bigStock)
---function to pippet the same reagent in many wells
---function to transfer one miniprep from STAGE1 plate into STAGE# plate
Digest block: (Input--the destination wells from the dilution block & stock of digest cocktail; output - destination wells)
Ligation block...

--NinaRevko 21:30, 10 June 2009 (UTC)

Nina 15 June 2009

The general meeting took place during regular Monday hours. Presentation of three projects left everyone with full-filling thoughts that something great is happening in our group and that people are totally not familiar what everyone is doing. This meeting and the upcoming Thursday meeting will keep everyone up-to-date and provide certain info-sessions on ongoing projects.

Nina 17 June 2009

I had meeting with my advisor. It took me about 40 minutes to put my thought and my code in order to present it and to talk about it. After the meeting I decided to work on the upcoming presentation that I had to make on Thursday. I spent some time working on presentation. The thoughts start coming in order and new fresh ideas about how the code is supposed to work, developed. I came to the conclusion that my Friday deadline will be missed but that I could finish by Monday...

Nina 20 June 2009

Last week the directions of what to do were clearly stated, the protocol for assembly procedure was obtained and several meetings with Doug Desmore and Chris Anderson was held. The part of the last week and this week I have been working on the assembly plugin.

Ideally my piece fits in the following scheme and should communicate with database (will be implemented later) and algorithm manager:

Nina Revko - ideally...

The work flow of the currently implemented changes will support the following operations:

take in SDS tree->process it in 3 arrays with data and one array with stages
based on a stage given by user, the program will pull out all resultant nodes together with lefty/righty parts
taking into account the future use of the part (as lefty or/and righty or as final product), the resultant nodes are sorted in the order of lefty/none/righty and will be put in wells of the reaction plate in that way
the initial well assignment to stock, dilution, reaction plate for a single stage is performed by the first method based on resultant usage
BigStock plate is currently hard-coded and holds dilution buffer (A5/A6) , digestion mix (B5/B6) and ligation mix (C5/C6)
one to many non-empty assigned/(modify this to do assignment for wells)
redundancy check for the stock and dilution plates performed, wells reassigned (3 functions)
- destinations and assignments scheduled for destinations are modified and reassigned
convert everything to 3 files for dilution, reaction and ligation processes
create user file - instructions for user

More graphical presentation of what the program should do is below:

Nina Revko - part1

Nina Revko - part2

The basic things to keep in mind:

min volume to pipette from single channel is 3ul (for accurate pipetting need 8ul in a well
max -"- 20ul
robot does mixing and changing of tips automatically
preferably stuff from Big Stock Plate goes in wells first (email Chris to ask whether it's important)
allow to integrate between pipette in rows or columns (specificity of the plate in our case, defined by user)

Upcoming work:

convert destinations to destination parameter class
finish cleanUpRedundancy function
modify it to keep track of well assignments
debugging, debugging, debugging
go in wet lab to test it
create GUI with possibilities of user-defined properties like to which file to save; to pick a stage, etc.

Nina 28 June 2009

For the past week I was working on fixing bugs. Over the week my program was able to produce correct output files with no errors =) Hooray!

On Friday, I went to wet lab and found out that they want more from my program that the piece that I made was not enough for them to do the testing. I was a little bit disappointed and worked a lot during week-end fixing and reorganizing pieces. I added:

a sorter for the resultant parts and populating the reaction plate besides lefty/righty, also according to 6 types of antibiotics
created an option for user to read in the stock plates from the text file (includes the possibility of having multiple stock plates)

Still to work and to do before showing up in front of the wet team:

do automatic plate assignment (currently hardcoded)--it is required for the multiple plates
do the file output for plating
do the user choice for antibiotic and their reassignment--by user!!!--it should be somewhere in tree

--NinaRevko 07:18, 29 June 2009 (UTC)

Team:Berkeley Software/NinaNotebook