We need the classic browser back around until the new browser is actually capable of allowing us to perform the same tasks as before, when we design and do analysis.
The classic browser is stress tested during many years. Nando and Jnicol have fixed its biggest problems so it is now supporting our work in an easy manner. This is not yet the case for the new browser.
While the new browser has cool new options, many of the most basic functions are still missing.
We need to be able to see the design structure - else we can’t make good use of the results from the earlier round to improve designing from this round.
We need to be able to view design description and
copying out sequence to modify designs and be able to experiment on
them. All these are things that are crucial for designing and analysis. This not being possible, gets in the way of us making good use of the lab results we have gotten back.
This is a problem!
Please come with your input. What options do you miss? What things would you like to see? Lets help Omei work out the wrinkles.
For many of the latest archived labs, it is not possible to see the 2D designs structure. We depend on them for analysis. Without the design structure, we can’t learn from past results to improve on current round.
This is already a problem as I now see even fewer of the new lab designers use past results for designing. We get a lot of from scratch design - which is good - but without being able to see and learn from the earlier results, designing is blind and we are not benefiting as we should from our precious lab results.
2D design structure as seen in the classic browser
When I refer to a design I modify, I typically leave a link back to the original design in my design description.
Leaving a link to the design I get inspired from is both a courtesy to the original designer, but also a help for analysis when we get the data back. Then I can easier see if what I intended really did work compared to what I started from.
Idea: If copying out sequence and referencing URL, and original score could be done in one go - in other words supported by the interface, that would be even better. We still need to be able to get either of these individually.
LABS, Project ID’s, puzzle ID’s Design(solution) ID’s.
Example LAB: Next Generation Riboswitches On Chip, (R1).
Project ID# 5851792.
Exclusion NG 1 Puzzle ID# 5851774.
Exclusion NG 2 Puzzle ID# 5851780.
Exclusion NG 3 Puzzle ID# 5851784.
Same State NG 1 Puzzle ID# 5851785.
Same State NG 2 Puzzle ID# 5851787.
Same State BG 3 Puzzle ID# 5851791.
The Project ID# is the alternate description of the Lab Name.
This lab contains 6 sub-labs.
The puzzle ID# is the alternate description of the sub-lab name.
The sub-lab has a list of Design iD’s for that sub-lab.
The Design id’s are the individual lab shape designs for the sub-lab.
Project ID#, Puzzle ID#, Design ID# is the hierarchy.
Original (old) URL format:
Goes to the Lab description page which should include the subl-lab icons.
Goes to a list of the design ID#’s in the puzzle ID sub-lab.
The “/“ symbol must be at the end of the URL for a successful search.
It would be helpful if there was a spreadsheet to reference past labs to ID numbers :)
I am currently working with Nando to get the 2D structure into the browser by embedding a reduced-functionality version of the flash applet there. I have two different UI possibilities in mind and could use some player feedback. But I'll post that in the https://getsatisfaction.com/eternagame/topics/new-lab-data-browser-for-eterna-medicine topic.
Ok, really this solution is probably less good than just having all the favored columns remembered by default.
Note that your preferences are stored in what HTML5 calls "local storage". Is it possible that you routinely work in "incognito" mode? If so, that would account for your preferences not being saved. The HTML spec requires that the browser clears out local storage data when the current session terminates.
If that isn't your issue, let me know and we'll figure out what is going wrong.
Less data viewable in the web browser compared to the flash browser
While the classic browser has way too much space in its data columns, I can still see far more both of the data columns and the sequences per lab. Which I like.
Flash, 40 sequences, sequence list fills 2/3
In the web browser, the sequences fills more and I can see fewer off them. This leaves me with less data columns on the side.
Web, 30 or really 29 sequences, sequence list fills 3/4
What is the greatest promise of the web browser is if one could view the sequence list alongside a design structure drawing and still have room for one or two data columns. The sequences filling too much leaves very little room for this. All extra space would be helpful for making the structure drawing bigger.
Some of the versions of the Data Browser have held the 40 sequence view. And I really liked it.
However I can't find the nupack one in the spreadsheets and as such it doesn't get into the web browser.
I would like to get kcal into the web browser. I have found it helps me for analysis.
I have found that the small boxes with info about which switch elements needs to be present in what state are not there. It holds great value to know, both to see if the puzzle fulfills demands - also of the simulation. At the same time this teaches us about the quirks of NUPACK. When we can see when lab allow things that simulation disagrees with. I'm in chrome.
The same puzzle in the classic browser
One of the tools I value the most in the classic browser is the sorting function. It's invaluable when it comes to distill what is working.
What one can do is click on any design of interest and get the data sorted by their similarity to this design.
It is by far the tool that tells me most, when it comes to comparing similar designs and see which small base changes are the most important and why. However it is not yet an option in the new browser.
I have earlier given an intro to the sorting function. The same document contains ideas for how to use it.
I opened the settings and Show Numbers was checked. I unchecked the box, went back to the puzzle, than back to the settings. Rechecked the NT numbers selection. The numbers then appeared in the puzzle OK.
New players have a hard time when the numbers are not shown.