dreichlab / waldo Goto Github PK

Sometimes we add in a select number of samples, either to a run that has a plate or to a new run. These samples can be from previously sequenced plates where the sample seems to have been accidentally omitted, or is a small experiment or something. so need to be able to add these somehow

The next I5 offset should be computable from the existing capture and raw plates.

Zhaos DB had a little calendar pop up whenever you were in a field that required a date, and was set to default show the current date. then you just clicked it and it filled in the date in the correct format. this would be nice since it is easier and should stop mistypes.

do whatever is required to remove the checkbox on this page
Needs sequencing: True for new plates. False for plates sequenced before website switchover.

We sometimes re-amp a library (due to low volume). This results in the library living in the original plate, as well as on a new plate in a well with a new nanodrop value for this plate. So we need to be able to show that an S-ID library was re-amped, whats the name of the new plate its on, what well is it in, and what is the nano value

Need more specification

Can we have WALDO make our dilution files for us. When we upload the nanodrop values, we then typically dilute our libraries to a standard concentration. so could WALDO do the math for us for a plate and then create the file?

plates starting from previously used Extracts in our lab. already have an S-ID

currently stops at Library Batch info, so need to add Capture and Sequencing info. and probably need to assess what info is shown when using the LookUp, specifically has been asked that a link to the Photos would be added to this page

Show remaining powder, lysate, extract

this can be one of the very last things looked at for WALDO, talk to Kim about ideas to make it easier to use this page for tracking of plates and boxes
Current Ideas/Notes

1. need to be able to edit multiple plates/boxes at once in regards to locations (both which freezer they are in, as well as shelf, rack, drawer in the freezer)

plates starting from previously used Lysate in our lab (already has an S-ID)

The next barcodes used in library batches should be computable from the existing batches.

We currently don't do this, but we should make sure to keep the door open just in case, unless Nadin says otherwise

plates starting from previously used Powders in our lab (already have an S-ID)

Add the ability to edit the ESS in this page - edit if theres wrong info, as well as having columns added that allow us to indicate info regarding specific samples. this way we can stop sending emails, and instead notate in WALDO whatever is needed and then Adam gets the ESS from WALDO instead

Have a display on the page that gives us a quick idea of what we have in the queue

1. Number of High and Low Complexity
2. Number of Drill and Sandblast

Can we make the Extra Powder Box Number some sort of dropdown field instead of typing. That way people can't write in weird strings of text. and are forced to choose OCR/NCR/FCR and then a number. And then the database will create the string OCR_EPB_## from what is chosen in the dropdowns

The results object is basically designed to handle analysis for single libraries. We need to replace this with a structure that will handle merges of libraries for an individual.

Add:

1. In Progress
2. Closed

we need to be able to move samples and then add samples that were previously captured into the empty well we just created

Sometimes we get already barcoded libraries and just go into Capture with them, so need to be able to add in new samples at the Capture stage and give them an S-ID. Note, these could have different barcodes than what we use, so need to be able to add that info into WALDO as well

We need to be able to enter in Extracts that were made in a different lab and sent to us, these don't have an S-ID yet and don't exist anywhere in WALDO, so need to get one assigned

We currently have an excel that lives in Teams that tracks the Reagent information of reagents we use when we do an extraction. So we would like to have this exist as fields in the headers for Lysates and Extracts so we can retire the excel in Teams

this page is very cluttered, can we make it look like the Library Protocol/Capture Protocol pages?

Sometimes we take a library and do another Raw sequencing of them. usually not a full plate, and typically use different iP5s than our standard

the main page for Powder Batches, Lysate Batches, Extract Batches, Library Batches, Capture Batches, Sequencing where it lists all the batches and relevant main info. we would like to be able to download a spreadsheet that has all that info for each of these pages

remove the Capture Positive from these plates. And make it an additional PCR Control

There are two different kinds of single stranded sequencing.

1. Both indices added at library stage
2. One index added at library stage and the other added later

Need to alter displays, forms, and spreadsheets to show indices.

Can we move the Plate ID from the sample tables up to the header info that affects the whole plate, since this is the label on the FluidX plate and so is the same for each sample on the plate.
Only issue with this, is that we still want the Plate ID to show up next to an S-ID if looked up. so don't know if this is possible.

We might do plates where we take a bunch of samples that need to be recaptured and put them all on one plate to get them done. So we need to be able to do what we do for Crowds/Mobs/Bands, where we submit a file of a bunch of S-IDs and have them layout onto a Capture plate (TW or RW)

Same as Lost Powder, this is a page that we need to work on to make it more usable for the wetlab. unknown how it works at the moment

Currently whenever we find a sample that needs to be recaptured, we put it in an excel that lives in Teams with the relevant info we need in order to recapture it. So at some point we would like to have this list exist in WALDO, with the functionality to add to it in WALDO, and when samples are recaptured, that the list updates itself with the information to show its been dealt with

The images of our plates in WALDO, the text bleeds into each other due to size of font

can we add underneath CleanUp robot in the header

1. CleanUp person
2. CleanUp date

Add project table
Add many-to-many relationship between projects and collaborators
Add many-to-many relationship between projects and samples

Reagent Batch/Bait needs to allow for decimals.
1240k+ and Big Yoruba bait uses labels such as 1.2.3.4, so multiple decimals need to be allowed

A small little field on the main page of the powder batches that tells us how many samples are set to the status "Ready for Plate" for each complexity. so we don't have to do the math to figure out if we have enough samples to make a lysate batch

Bands, Crowds, and Mobs typically have multiple libraries made of the same sample and so to save on capture reagents, we pool these back together once they've been barcoded. So we need to be able to combine multiple Bands/Crowds/Mobs together into one Blob plate of these pools.

Add:

1. In Progress
2. Closed

Table of ALL info for each sample at this stage. For captures, this would include info from the sample prep queue, powder batch, lysate batch, extract batch, library batch, and capture or raw batch for each library on the plate.

For powders arriving from collaborators, allow preweighed values from powder queue to propagate to layout. Null values are not preweighed.

Sometimes we are given samples (already powdered, or as extracts), and then later on its determined to send the sample for C-14. When this happens, usually we are then sent the piece and we take photos and then submit for C-14. so we need a way to add photos to S-IDs that don't exist in a powder batch (as this is the only spot at the moment in which we can add photos).

We need to work on this part and make it more functional for our needs

can we have some of these fields give us a dropdown with options based on the Platform chosen? or something along these lines. Read length at the moment is always the same value, but we always have to look at older submissions to remember what to type here

The number of estimated lanes for sequencing run should allow fractional values.

We currently have an excel that lives in Teams that tracks the reagent information of reagents we use for our library preps. We would like to retire the excel and have all this information tracked in WALDO for each plate

each field would allow us to filter by whatever is in the field, and we can do this on multiple fields at a time, and then clicking download spreadsheet would download a table of only the samples that fit the dropdowns chosen

For files that we download from WALDO, is it possible to change the file names to put the Batch Name first, and then the info such as what page it was downloaded from? This way, if I download all the files for Charm.39 (Lysate, Extract, LibPrep, Capture, Sequencing) they would all be grouped together on my desktop since they share the same first info Charm.39.