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What happened: when scrolling with inertia on iPad the canvas stops rendering until the scrolling stops.

What should happen: when scrolling with inertia, the canvas should continue to render

What happened: When the user closed the Gentle tab, or when Gentle launches and closes old sequences, old work can be lost. (e.g. the user didn't think about whether they saved to synbiota. Their data could have been lost.)

What should happen: If the user closes the browser for gentle, or changes the url (e.g. someone searches google or something), there should be a warning the comes up saying: "Sequences have been modified. Save changes to Synbiota?" with three buttons: [Don't Save], [Save], [Save All].

For non-synbiota version: "Sequences have been modified. Download your changes to local?" This would automatically export the unsaved file as a .sybil file to local downloads

What happened: When I opened the "information" Annotation dialogue for a sequence and inputted a description, I tried to delete a mistake using 'delete' key and it wouldn't work. I could highlight the text and delete it using the delete key

What should happen: I should be able to delete text in all dialogues using the delete key (with or without highlighting it)

Presently there is no way to highlight a sequence (standard colours - yellow/red...)

What happened: If I drag and add a part in the top work-box I cannot delete it

What should happen: There should be a way of deleting a part - perhaps there could be a small trashcan that a part can be dragged into

Calculator forms for common lab tasks, e.g. ligation or photometric DNA concentration measurements. Calculators should allow to be "seeded" from open sequences. Additionally, show data tables (codon tables etc.).

Use i18n for all interface elements

What happened: Within the designer feature, I tried to drag a part into the 'work box' at the top. The part would "grab" and "drag" but when I released it in the 'work box' Gentle froze and the part froze not quite inserted in the correct spot.

What should happen: part should drop into the work box

Suggested preliminary annotation types to be added:

Ori
Selection

What happened: I opened a sequence from Synbiota and then I had another sequence loaded with NCBI imported. With the NCBI imported file loaded, I opened sequences in Designer, everything appeared fine. I saw the right sequence/parts and that same sequence/parts in the top "work-box". Using the 'loaded sequences' dialogue I deleted the "designer" sequence in hopes of closing it and returning to the NCBI loaded sequence that I was viewing before launching designer, but the screen went white.

What should happen: When clicking the delete button, the designer file should close and another loaded file should appear.

What happened: The user created a new sequence within a project in Gentle and pressed 'save to synbiota'. The user then changed the name/description of the sequence and saved to synbiota. This resulted in two sequences appearing in their project. Once "un named" sequence and one "named (with the changes they made)". Every new save results in a new sequence in the user's Synbiota projects section.

What should happen: The user should create a sequence and all changes and saves to that sequence should result in only one sequence visible in the projects. Other saves to synbiota could be saved as versions. This suggests the need to have a "Saved Versions" button next to the sequence in the project that, when clicked, results in a popup with clickable ["name" "date/time edited" "edited by user"] links. When clicked this opens that version in gentle.

This problem is treading on Versioning territory!

Brian are your free to start tackling the versioning?? Przemek, is there an easy fix for now?? Magnus, any thoughts??

@magnusmanske @szeryf

Presently the user must use menus at the top of the page to complete certain functions. What is the possibility of implementing a right click 'contextual menu' for Gentle in desktop devices. Features like 'annotate', 'highlight'... could all be here...

What happened: When open and refresh Gentle (on Mac/Chrome) I can drop in a file and it loads fine. If I try to then drop in another file, it does not load into Gentle, but it loads in the browser as a .txt file. If after adding the first file I refresh the browser, then the next file loads perfectly. If I then refresh the browser again and drop in the next file it loads perfectly.

What should happen: Multiple consecutive files should be loaded without having to refresh the browser in between.

What happened: In the desktop version you can click and drag the yellow highlighted region of the context window to navigate to a new position. This is inactive on Mobile

What should happen: This feature should be active on mobile (iOS and Android)

Make sure to backup the AMI so that we can restore in case of disaster.

Presently when scrolling on iOS Safari, the canvas doesn't render until the inertia function completes. Is there a work-around for this?

What happens: when a note is created the "title" is displayed over top of the sequence and an annotation line extends over the entire DNA sequence that was selected.

What should happen: the Note feature is distinct from the other annotation features because it is an active tool for communication. Sometimes the note will be long and sometimes short. We need a way of showcasing that a comment is present at a particular sequence, but it should be collapsible/expandable so not too cover the editing area.

-Perhaps after saving the note a small note icon is situated next to the beginning of the note annotation line (next too the comment title) and when the user clicks on the note icon, the note pops-up and becomes visible.

-there should also be a delete note icon directly next to the note icon for easy removal of the note.

-the Synbiota user who created the note should be recorded

-the time the user recorded the note should be recorded.

I imagine the reason we can't do cut and paste on iOS is the same reason we can't use the native keyboard. Is this something that can be fixed with additional development, or is it an issue with the way text on a canvas is an image of text, not actual text?

Is this something I can get an additional Java developer to assist with?

Run online blast on selection or entire sequence. For DNA and amino acid sequences.

Implement undo/redo for all actions.

There is presently a close sequence feature. There should also be a "close all sequences" feature that closes all loaded sequences.

What happened: when I use the search feature to find a sequence and then click on one of the suggested regions, that sequence is highlighted in yellow. If I touch the screen or try to scroll, the yellow disappears and I lose the spot.

What should happen: I should be able to scroll up and down whilst the sequences stays highlighted. Perhaps a double touch should remove the highlighting

What happened: When I have a loaded sequence/sequences in designer I try to drag them into the top work-space, but they are not draggable

What should happen: The parts should all be draggable (just like in the PC/desktop version)

When I delete BPs from the editor window the side context window does not update to represent the new document. Could it be re-rendered on cut, delete, type and paste?

What happened: The user was trying to Name/add description about their sequence. The user first searched through the 'file' 'tools' 'sequence drop down menus and then stumbled across the annotation dialogue.

Solution: Add an option in the File drop down, "Name Sequence" that and when clicked could result in the same annotation dialogue opening.

'nuf said

What happens: when I create a note, I have the opportunity to enter a title and a description.

What should happen: a note should just be a single entry - no need for a title. If possible, the user who created it should be recorded and also the time they created it.

An extension of the sequence information dialog "Annotation" tab to view and edit details of an annotation.

Load phylogenetic data formats. Generate trees from Alignments. Display trees in browser.

What happened: After loading multiple parts into Gentle and entering "Designer", some of the options in the top nav bar are no longer needed.

What should happen: After entering "Designer", a "Designer" specific Nav bar should be present: 1) "Sequence" is no longer needed; 2) "gear icon" is not needed; 3) "sequence info [little i icon]" is not needed; 4) "expand/collapse context" arrow icon is not needed

In order to load Gentle quicker and give a super awesome user experience, can we please implement Minifying!

Add a dialog to run endonuclease digestion with one or multiple enzymes. Preview resulting fragments. Allow creation of (some) fragments as new sequences.

Simulate DNA agarose gels for restriction endonuclease digests and PCR modules. Allow combination of multiple such results in a single gel. Allow for rearrangement of lanes. Allow selection of standard markers (DNA ladder). Allow for different agarose percentage. Show different intensity of bands based on expected DNA concentration (known for markers).

Amino acid sequence module. Show protease cut markers. Show automated annotation, including secondary structure prediction, Chou-Fasman, coiled-coil prediction, etc. Allow backtranslation into DNA, based on organism and/or codon optimization.

There is room for optimization of the copy/cut/paste feature in Gentle (especially for mobile).

What you did: Tried to copy/paste some DNA code using the copy/paste function on mobile.

What did happen: I select some code to copy/cut and click on file --> copy and a dialogue opens showing the code I selected. I close the dialogue, choose a point to paste the code into (double click into edit mode) and click file--> paste, a dialogue with the 'paste' code opens, but it is blank. Ideally, this would have the code I just copied, so I can simply click paste.

What should happen: Ideally, there isn't any dialogue that appears and the copy/paste is done behind the scenes - it is a standard copy/paste function. (the shortcut keys work on laptop/desktop, but unfortunately this doesn't work on mobile!

Hey Magnus, I hope these bug reports are useful. Might as well make a list in here I guess ;-)

• Cut and paste are not working on the desktop Safari. Works great in Chrome though!

What is it: issue when annotating a selection after highlighting

What happens: When I highlight from the top of the page downwards (from low nucleotide number to high nucleotide number) and annotate, everything works fine and the context window shows the annotation perfectly. When I highlight the sequence from the bottom of the page upwards (from higher nucleotide number to lower nucleotide number) and annotate, the annotation block takes up the entire context window. When i reassess the annotation in the "annotation dialogue", it lists correctly.

What should happen: regardless of whether I highlight from low to high or high to low nucleotide number and annotate, the part show appear the same in the context window.

What happened: in order to add a note I have to embark on a long journey. Users will want to make many notes very often.

What should happen: adding an "add note" option to the context button will easily allow a user to create a note. By clicking this feature the user could be taken directly to the same "sequence info" dialogue where they could easily add their note and save.

What happened: The user made a typing error in the 'Annotation' dialogue and tried to delete the word using delete/backspace. It didn't work. It does however work when the tester highlighted the word and deleted

What should happen. The user should be able to name and add general description with the delete/backspace key stroke functional.

Read standard alignment formats. New "sequence" type to display alignments. Allow for DNA and amino acid sequences. Allow for re-alignment with built-in or external alignment algorithms. Allow manual optimization of gaps. Allow new alignments based on open sequences. Allow for alignments containing DNA and ABI/SCF-based sequences, with inline chromatogram display. Allow saving in standard alignment formats.

New "sequence type" for PCR. Start PCR from DNA selection. Design and optimize primers. Assisted primer editing for restriction endonuclease sites. Primer optimization (annealing temperature, length, GC, etc.). Generation of PCR product(s) as new DNA sequence(s).

What happens: after part of the sequence is annotated and the description and title are saved, the annotation can be Only be deleted in the "sequence info --> annotation tab"

What should happen: the user should also be able to edit That annotation (title, description) via the Sequence info dialogue

What feature exists: presently there are 4 buttons that allow you to change zoom of the context window

What feature should exist: a google maps like zoom bar. It is more intuitive.

also see #60

What happened: When I load many 'parts' into the top work-box in designer, once the screen is filled from left to right, the graphic then continues on a second line. When the second line is filled, I can no longer add parts.

What should happen: The top work-box should be scrollable and the parts should only be in only one line. This scrollable feature should be functional on both desktop and mobile

A mode for high-level design of DNA via drag'n'drop.

What happens: If I highlight some DNA and press the delete key, I navigate back to the previous website I visited. This might confuse the user if they are not in editing mode and try to delete.

Suggestion of what should happen: if the user has highlighted a sequence and presses delete, perhaps they should get a pop-up saying, "To delete this, please enter edit mode by double-clicking on a nucleotide" or something...

Perhaps we could get better canvas performance by pre-rendering the sequence text?

Interesting article with performance charts:

http://www.html5rocks.com/en/tutorials/canvas/performance/

Import of ABI and SCF (capillary sequencing chromatogram) format. New sequence type for displaying this type of data.

What happened: When the user launched Gentle and wanted to create a new sequence, previously opened sequence were still active in the browser and confused the user (he was using my laptop during the test!)

What should happen. When gentle launches, it should automatically close existing sequences.

Save sequences to Synbiota. Also, update to new API for opening files, once available.