core issueshttps://git-r3lab.uni.lu/minerva/core/-/issues2024-01-09T14:39:12+01:00https://git-r3lab.uni.lu/minerva/core/-/issues/1836Overlay files containing raw numerical data2024-01-09T14:39:12+01:00Luiz LadeiraOverlay files containing raw numerical dataIt would be nice to be able to upload overlay files with one more additional column containing the raw numerical data (without scaling from 0 to 1, or -1 to 1).It would be nice to be able to upload overlay files with one more additional column containing the raw numerical data (without scaling from 0 to 1, or -1 to 1).v18.0https://git-r3lab.uni.lu/minerva/core/-/issues/599Add possibility to create link from element to overview image2024-01-09T19:27:56+01:00Piotr GawronAdd possibility to create link from element to overview imagerequested by faiz.khan3@uni-rostock.derequested by faiz.khan3@uni-rostock.dev18.0https://git-r3lab.uni.lu/minerva/core/-/issues/278Search and zoom function2024-01-09T19:30:13+01:00Kerstin NeiningerSearch and zoom functionAfter hitting the search button, it is zoomed out completely (which is unfavourable in some applications). I would recommend that the default is not zooming out after a search. But to enable both (zoom out completely or not), an extra bu...After hitting the search button, it is zoomed out completely (which is unfavourable in some applications). I would recommend that the default is not zooming out after a search. But to enable both (zoom out completely or not), an extra button/checkbox that can be checked to enable a zoom out would be nice.v18.0https://git-r3lab.uni.lu/minerva/core/-/issues/225User should be able to change his data2024-01-11T07:14:35+01:00Piotr GawronUser should be able to change his datav18.0https://git-r3lab.uni.lu/minerva/core/-/issues/166Left panel - User data layout2024-01-09T19:34:36+01:00Marek OstaszewskiLeft panel - User data layoutIn the Info panel, User data is clumped together. This layout should be improved, if possible.In the Info panel, User data is clumped together. This layout should be improved, if possible.v18.0https://git-r3lab.uni.lu/minerva/core/-/issues/20Advanced search2024-01-09T19:42:53+01:00Piotr GawronAdvanced searchThere should be a way to perform advanced search.
Search should allow to limit results by type/name/annotation.There should be a way to perform advanced search.
Search should allow to limit results by type/name/annotation.v18.0https://git-r3lab.uni.lu/minerva/core/-/issues/2002Feature request: handle user overlays across projects on the same platform2024-02-20T13:46:46+01:00Marek OstaszewskiFeature request: handle user overlays across projects on the same platformCurrently, when new versions of a project are uploaded to the same MINERVA PLatform, overlays have to be manually transferred.
This is error-prone and time consuming, with data potentially propagating against users' intention. MINERVA sh...Currently, when new versions of a project are uploaded to the same MINERVA PLatform, overlays have to be manually transferred.
This is error-prone and time consuming, with data potentially propagating against users' intention. MINERVA should support easier handling of the user overlays within the same platform.
Suggested solutions:
Solution 1:
- user overlays are common across projects, visible for their owner on each project (on the same platform) the owner has access to.
- public/global overlays: a given overlay would be decided as public/global per project.
- challenge: removal of a single root overlay would result in removing it from other projects
- suggestion 1: allow this behaviour under a warning prompt
- suggestion 2: block a removal of an overlay until it's made private on all related projects
Solution 2:
- implement a functionality for user data transfer (in bulk) across projects
- challenge: this would be a manual solution, with data potentially propagating against users' intentionhttps://git-r3lab.uni.lu/minerva/core/-/issues/1657annotating should be a separate job that can be run at any time2022-02-28T14:06:08+01:00Piotr Gawronannotating should be a separate job that can be run at any timehttps://git-r3lab.uni.lu/minerva/core/-/issues/1616Add support for kinetics MathML functions2021-12-16T11:12:17+01:00Piotr GawronAdd support for kinetics MathML functionsFull list can be found here:
http://co.mbine.org/specifications/sbml.level-3.version-2.core.release-2.pdf
Implement at least those:
* arithmetic operators: plus, minus, times, divide, power, root, abs, exp, ln, log, floor, ceiling, fact...Full list can be found here:
http://co.mbine.org/specifications/sbml.level-3.version-2.core.release-2.pdf
Implement at least those:
* arithmetic operators: plus, minus, times, divide, power, root, abs, exp, ln, log, floor, ceiling, factorial, quotient, max, min, rem
* trigonometric operators: sin, cos, tan, sec, csc, cot, sinh, cosh, tanh, sech, csch, coth, arcsin, arccos, arctan, arcsec, arccsc, arccot, arcsinh, arccosh, arctanh, arcsech, arccsch, arccothhttps://git-r3lab.uni.lu/minerva/core/-/issues/1594rewrite API2024-02-29T14:52:38+01:00Piotr Gawronrewrite APICurrent API implementation is becoming hard to extend and maintain. Here are base points that should be considered when rewriting API:
* all input/output should be entity based json (except when passing file content)
* serialization shou...Current API implementation is becoming hard to extend and maintain. Here are base points that should be considered when rewriting API:
* all input/output should be entity based json (except when passing file content)
* serialization should be done automatically using Jackson
* patch/post/delete requests should handle properly simultaneous modifications of the objects (https://www.mscharhag.com/api-design/rest-concurrent-updates)
* when accessing collections use Pageable interface
* use JPA validation for input parametershttps://git-r3lab.uni.lu/minerva/core/-/issues/1480User Groups2021-06-09T11:22:02+02:00Matti Hochmatti.hoch@uni-rostock.deUser GroupsPossibility to put users into customized groups to facilitate assignment of access to projects, etc.Possibility to put users into customized groups to facilitate assignment of access to projects, etc.https://git-r3lab.uni.lu/minerva/core/-/issues/1276allow for automatic break of name text into few lines2021-04-20T11:18:43+02:00Piotr Gawronallow for automatic break of name text into few linesrequested by Guanming Wu wug[at]ohsu.edurequested by Guanming Wu wug[at]ohsu.eduhttps://git-r3lab.uni.lu/minerva/core/-/issues/1192automatic layout for non-layouted sbml2020-03-12T12:27:22+01:00Piotr Gawronautomatic layout for non-layouted sbmlwe can consider using graphviz (https://www.graphviz.org/) to improve automatic layout (keeping in mind separations of compartments, complexes, etc)we can consider using graphviz (https://www.graphviz.org/) to improve automatic layout (keeping in mind separations of compartments, complexes, etc)https://git-r3lab.uni.lu/minerva/core/-/issues/952Changes in the layout of the window "Select annotators"2024-01-09T15:25:17+01:00Ewa SmulaChanges in the layout of the window "Select annotators"Please change window *Annotate model automatically:* as below:
- adjust right side windows *available annotators* and *selected annotators*,
- move "Please click on selected annotator to display details at the bottom" next to the *Selec...Please change window *Annotate model automatically:* as below:
- adjust right side windows *available annotators* and *selected annotators*,
- move "Please click on selected annotator to display details at the bottom" next to the *Selected annotator* window, at height of the first annotator,
- shorten the let panel and place Copy from and dropdown list below the list,
- sort the list and categorised as per below. Please put spacing or linr between the categories.
hi @marek.ostaszewski Do you agree with theses changes?
![Screen_Shot_2019-09-13_at_15.59.41](/uploads/2516577fbf9ff495f7e08ad70e042ae0/Screen_Shot_2019-09-13_at_15.59.41.png)![Screen_Shot_2019-09-13_at_15.18.47](/uploads/ebcbcf4211fb3a205c8db64da151cb59/Screen_Shot_2019-09-13_at_15.18.47.png)https://git-r3lab.uni.lu/minerva/core/-/issues/699Search panel options (admin panel) - small amendments2023-12-21T14:04:41+01:00Ewa SmulaSearch panel options (admin panel) - small amendments1. Divide the table on two parts, with headers:
* Reactions
* Elements
Please review *Name* fields, "element" and "reaction" can be removed.
2. Please change "Show element title" in *Search panel options* tab onto "Show a pin"1. Divide the table on two parts, with headers:
* Reactions
* Elements
Please review *Name* fields, "element" and "reaction" can be removed.
2. Please change "Show element title" in *Search panel options* tab onto "Show a pin"https://git-r3lab.uni.lu/minerva/core/-/issues/486SBGN - activity flow2021-01-27T11:34:21+01:00Piotr GawronSBGN - activity flowDescription of the format can be found here: http://co.mbine.org/specifications/sbgn.af.level-1.version-1.2.pdf
We already use libsbgn library for parsing SBGN: https://mvnrepository.com/artifact/org.sbgn/libsbgn/0.2
Below you can find...Description of the format can be found here: http://co.mbine.org/specifications/sbgn.af.level-1.version-1.2.pdf
We already use libsbgn library for parsing SBGN: https://mvnrepository.com/artifact/org.sbgn/libsbgn/0.2
Below you can find SBGN AF mapping by Alexander:
> Here is the mapping between CellDesigner's Reduced Notation links and SBGN Activity Flow links. I use exact terms from the CellDesigner's Reduced Notation palette and the terms of the Activity Flow reference card (attached).
>
> Positive Influence -> positive influence
>
> Reduced Physical Stimulation -> positive influence
>
> Unknown Positive Influence -> positive influence
>
> Unknown Reduced Physical Stimulation -> positive influence
>
> Negative Influence -> negative influence
>
> Unknown Negative Influence -> negative influence
>
> Reduced Modulation -> unknown influence
>
> Unknown Reduced Modulation -> unknown influence
>
> Reduced Trigger -> necessary stimulation
>
> Unknown Reduced Trigger -> necessary stimulation
>
> In principle, the unknown (dashed lines) could be kept, it is okay not be strictly AF in this case.
>
> Please note that, as we discussed, we should not change the way you handle the internal model in MINERVA, >we should only modify the visual part when a user checks "Visualise in SBGN Activity Flow" box.
>
> This is the compromise we agreed on: modifying visually, not the model itself. Activity Flow is >conceptually a different language. For example, it would be tricky to try to present multiple state >variable in AF (and it is not needed, not the purpose of this language).
>
> When it comes from CellDesigner: normal pipeline but modified visualisation for AF if a user requests it >(works only for reduced notation, no processes allowed).
>
> When it comes from SBGN-ML, the mapping to CellDesigner Reduced Notation (or internal MINERVA model) is >possible, fewer problems there since in a clean AF we would not introduce state variables etc.
>
> Mapping from SBGN-ML AF to CellDesigner for links:
>
> positive influence -> Positive Influence
>
> negative influence -> Negative Influence
>
> unknown influence -> Reduced Modulation
>
> necessary stimulation -> Reduced Trigger
>
> Mapping from SBGN-ML to CellDesigner for entities: keep labels as they are, use auxiliary units to inform >on the type of shape to be used, for example, macromolecule, RNA, gene etc.Sascha HerzingerSascha Herzingerhttps://git-r3lab.uni.lu/minerva/core/-/issues/229enhancements to plugin API2017-11-08T11:32:09+01:00Piotr Gawronenhancements to plugin API* [ ] there should be a way to provide list of plugin urls in the configuration panel
* object passed to plugin should contain some meta information:
* [ ] BioEntity - should also implement getChildren, getCompartment, getComplex wh...* [ ] there should be a way to provide list of plugin urls in the configuration panel
* object passed to plugin should contain some meta information:
* [ ] BioEntity - should also implement getChildren, getCompartment, getComplex when applicable
* [ ] Reaction
* [ ] Annotation
* [ ] MiRnaDb
* [ ] DrugDb
* [ ] SearchDb
* [ ] ChemicalDb
* [ ] Marker
* [ ] Surface
* [ ] DataOverlay
* [ ] getAllBioEntities(filter) - this method should contain optional filter parameter that can contain type of bioentity
* [ ] addContextSubmenu({submenu}) -allow user to create context menuhttps://git-r3lab.uni.lu/minerva/core/-/issues/34multiple links from single area in biolayout2019-02-20T15:08:27+01:00Piotr Gawronmultiple links from single area in biolayoutWhen we process biolayout images the clickable regions should allow to link to more than one region on the map.When we process biolayout images the clickable regions should allow to link to more than one region on the map.https://git-r3lab.uni.lu/minerva/core/-/issues/33entrez annotator - add uniprot when annotating2019-02-21T14:26:21+01:00Piotr Gawronentrez annotator - add uniprot when annotatingThis is not as easy as it sounds.
Entrez data model is so complicated/messy that finding uniprot there is a bit challaning...This is not as easy as it sounds.
Entrez data model is so complicated/messy that finding uniprot there is a bit challaning...https://git-r3lab.uni.lu/minerva/core/-/issues/18export to excel file2018-08-27T10:35:25+02:00Piotr Gawronexport to excel file