Ribbon | genome browser that shows long reads | Genomics library

 by   MariaNattestad JavaScript Version: 1.1 License: MIT

kandi X-RAY | Ribbon Summary

kandi X-RAY | Ribbon Summary

Ribbon is a JavaScript library typically used in Artificial Intelligence, Genomics applications. Ribbon has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

Please cite our preprint on the BioRxiv: Ribbon is an interactive web visualization tool for viewing genomic alignments of short/long reads or assembled contigs to any reference genome. Ribbon is available online at genomeribbon.com and can even read large bam files straight from your computer without a local install.
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              Ribbon has a low active ecosystem.
              It has 190 star(s) with 27 fork(s). There are 15 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 0 open issues and 28 have been closed. On average issues are closed in 184 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of Ribbon is 1.1

            kandi-Quality Quality

              Ribbon has 0 bugs and 0 code smells.

            kandi-Security Security

              Ribbon has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              Ribbon code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              Ribbon is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              Ribbon releases are available to install and integrate.
              Installation instructions are not available. Examples and code snippets are available.
              Ribbon saves you 263 person hours of effort in developing the same functionality from scratch.
              It has 639 lines of code, 10 functions and 15 files.
              It has low code complexity. Code complexity directly impacts maintainability of the code.

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            Ribbon Key Features

            No Key Features are available at this moment for Ribbon.

            Ribbon Examples and Code Snippets

            Gets the value of the ribbon environment variable .
            javadot img1Lines of Code : 13dot img1License : Permissive (MIT License)
            copy iconCopy
            private String getRibbonEnv(String[] activeProfiles) {
                    String[] displayOnActiveProfiles = jHipsterProperties.getRibbon().getDisplayOnActiveProfiles();
                    if (displayOnActiveProfiles == null) {
                        return null;
                    }
                    L  
            Enable ribbon filtering .
            javadot img2Lines of Code : 4dot img2License : Permissive (MIT License)
            copy iconCopy
            @Bean
                public IRule ribbonRule(IClientConfig config) {
                    return new AvailabilityFilteringRule();
                }  
            Non ribbon rule .
            javadot img3Lines of Code : 4dot img3License : Permissive (MIT License)
            copy iconCopy
            @Bean
                public IRule ribbonRule() {
                    return new WeightedResponseTimeRule();
                }  

            Community Discussions

            QUESTION

            Word VBA Insert a table of contents building block
            Asked 2021-Jun-14 at 02:54

            I am trying to insert a table of contents into a Word document using one of the built-in building blocks that define a table of contents. When I record a macro and insert a table of contents the macro recorder gives this line of code:

            ...

            ANSWER

            Answered 2021-Feb-17 at 03:54

            The macro recorder is just a starting point. The sample you posted is dependent on a very specific path to the building block template, one that includes your user name and the language you are using (1033 is U.S. English) and the version of Word (16 for Word 2016 and 2019). In addition, the building blocks template location does not have a VBA shortcut to reach it.

            What will work more reliably is to insert the table to your macro template or a document based based on that template. Select the table, then choose Insert>Quick Parts>AutoText>Save Selection to AutoText Gallery. You can set the name to whatever you prefer. Set the Gallery to Table of Contents. OK out, then delete the table sample.

            Now you can use simpler, more reliable code like this:

            Source https://stackoverflow.com/questions/66235138

            QUESTION

            How to design a model for contour recognition? In particular, how to shape the output layer?
            Asked 2021-Jun-10 at 10:11

            I want to design and train a neural network for the automatic recognition of the edges, in some microscopic images. I am using Keras for a start, I may consider PyTorch later.

            The structure of the images is rather simple, with some dark areas, and some clear areas, relatively easy to distinguish, and the task is to select the pixels of the contour between dark and clear areas. The transition between dark and clear is gradual, so my result is not a single line of edge pixels, but rather a 10 or 15 pixels wide "ribbon" at the edge.

            I have manually annotated 200-something images, so for each image I have another image, of the same size, where the pixels of the contours are black, and all the other pixels are white.

            I have seen many tutorials on how to design, compile and fit a model (a neural network), and then how to test it, using the manually annotated data.

            However, most of the tutorials work on problems of classification, where the number of neurons in the output layer is the number of categories.

            My problem is not a problem of classification, and ideally my output should be an image of the same size of the input.

            So, here is my question:

            What is the best way to design the output layer? Is a layer with a number of neurons equal to the number of pixels the best idea? Or this is a waste, and there is a more efficient way?

            Addendum

            1. The images are "easy", but it is still difficult to find the contour pixels, so I believe that it is worth using the machine learning approach.
            2. The transition between dark and clear is a little gradual, so my result is not a single line of pixels on the edge, but rather a band, a 10 or 15 wide ribbon of edge pixels. Since I am after a ribbon of pixels, my categories should be "edge" and "not-edge". If I use the categories "dark pixels" and "clear pixels", and then numerically find the pixels between the two areas I do not get the "ribbon" result, which I need.
            ...

            ANSWER

            Answered 2021-Jun-10 at 10:11

            The short answer is "yes": it is a good idea to have as many neurons in output as you have in input, i.e. to output an image with the same resolution of the input images.

            The network architecture will have an input layer with a neuron for each pixel, then typically the hidden layers will shrink to less neurons, probably with convolutional layers, and then some more layers will re-expand the number of neurons, up to the output layer, which in principle may have the same number of neurons as the input layer.

            The most common architecture in this type of problem is the U-net architecture, described in the article "U-Net: Convolutional Networks for Biomedical Image Segmentation", by Ronneberger, Fischer, and Brox, published on the open arxiv: https://arxiv.org/abs/1505.04597.

            [

            Source https://stackoverflow.com/questions/67874428

            QUESTION

            How do precisely place and align controls on Access forms (Align does not do this)?
            Asked 2021-Jun-10 at 00:16

            I have a Microsoft Access (Office 365) form. I need the controls to be neatly placed on the form.

            For example, in the Access Form Design View below, the "Residential" label and the rectangle around the checkbox both have the same Left and Width. The Left property was set by using the Align - Left option of the Sizing & Ordering group of the Arrange ribbon tab.

            • I have looked at the padding and margins for each control. This has no effect on control placement.

            • Is there a way to compute the Top and Left placement for a control? I tried Top + Height + 2*BorderHeight with all padding and margins set to 0. This did not improve the situation.

            • One of the biggest problems is the absence of support to precisely position controls independently from the labels.

            • Is there a third-party tool that can be used to design Access forms? Form layout seems to be time-consuming aspect of Access.

            ...

            ANSWER

            Answered 2021-Jun-10 at 00:16

            First up, leaving out the WHOPPER of a detail that this looks to be a continues form (multiple items form) is a huge detail.

            Furthermore, forms created by the wizard ALSO include what is called the layout control. Now for reports, and continues forms? This is in most cases a fantastic option - you can re-size a control and ALL OTHER controls move + re-size for you. This can save you hours and hours of having to painfuly layout controls on a form.

            However, for specialized layout - or layouts that are not "just" one control to the next? Then yes, you want to REMOVE the layout control.

            It as noted would have helped the readers here if you showed more of that form.

            So, a typical multiple items form will look like this (and that orange border bar, along with the HEADING part of the form ALSO shows that layout control system in action.

            So, what I suggest for more specialized layouts? Remove the layout control.

            So, WHEN you have a layout control in use, you see this:

            So in above, when you click on that detail row - note the orange bar and NOTE VERY careful the "+" sign. (the blue arrow points to it). So click on that + sign.

            So click on the + sign - all of the controls in that layout will now show (orange lines around all controls in that layout).

            So click on that + sign.

            Now in ribbon (arrange tab) select remove layout:

            Like this:

            At this point, the orange bars will go away.

            At this point, you can free form move around the controls any where, and any way you want. JUST keep in mind that of course then if you say re-size or move around a control, the other controls WILL NOT automatic move for you anymore. As noted, for some cases, you really don't' want the layout. This tip/suggest also applies to basic forms - you want again to remove the layout control - and you often do this for regular forms.

            As noted, for a report, or a continues forms (multiple items form), then often the layout control is your best friend. But, removing it? Now you on your own - you have to place things just as a you want - no layout helper will be active.

            Source https://stackoverflow.com/questions/67905360

            QUESTION

            Automatically load and start runtime of Office-js add-ins for all documents
            Asked 2021-Jun-06 at 19:14

            I'm developing an office-js add-in that needs to run automatically (without user interaction) every time any Excel document starts. I have configured it to use a shared runtime. This capability exists for VSTO add-in which load when Excel starts but seems to be missing for Office-js addins.

            I only found two possible solutions, but they don't work that well:

            1. When the add-in runs for the first time in a document, set Office.addin.setStartupBehavior(Office.StartupBehavior.load) so that the add-in loads automatically for the document.

            Issue: the add-in needs to be manually inserted once (the user needs to click on the add-in ribbon once per document). This setting only applies to the current document. Not practical since users first need to interact with the add-in for every new document.

            1. As Excel opens a new document, use a VSTO add-in to insert the add-in by editing the document using OpenXML following this article https://docs.microsoft.com/en-us/office/dev/add-ins/develop/run-code-on-document-open.

            Issue: Excel blocks I/O for documents as they are opened. For local documents, I found a way to write onto them as Excel writes on them, but when the documents are saved on OneDrive, any stream with ReadWrite attributes can't get access. So this solution is not working very well.

            Is there a workaround possible?

            ...

            ANSWER

            Answered 2021-Jun-06 at 19:14

            No, there is no other way to get Excel web add-ins loaded automatically.

            Source https://stackoverflow.com/questions/67803278

            QUESTION

            Ribbon load balancer client not disabling in Spring boot 2.4.3 & Cloud 2020.0.1. Using Consul for load balancing instead
            Asked 2021-Jun-06 at 15:13

            I'm currently working on a microservices application for my internship using Consul for service discovery and feign clients for communicating between the services. When we started working on the existing project which already was built using microservices, we upgraded Spring boot to 2.4.3 & cloud to 2020.0.1, so that we could make use of Java 15 to use records instead of normal classes for dtos. The problem we have now is that, whenever we make a call to a composite service, that will try to retrieve data from multiple services (for example users and teams service), that we get the following stacktrace:

            ...

            ANSWER

            Answered 2021-Jun-04 at 07:23

            Can you try excluding ribbon dependency as shown below

            Source https://stackoverflow.com/questions/67717907

            QUESTION

            Calling an async method inside another async method does not work in office js. Using the command script used from the Ribbon in a web browser
            Asked 2021-Jun-04 at 08:31

            Do you know why this function called from my script commands.ts which is a script used by the commands in the ribbon wouldn't work?

            I am creating an Add-in for Outlook and I am calling the method "join" which is triggered when the button from the ribbon is clicked. The issue I am having is that when I am in the browser the method "replaceAsync" never gets called so the notification is never added to the screen. If I run the application in Outlook desktop the notification shows absolutely fine (image 1). This is the method I am using, could you advise if what I am doing is correct and do you know what could be reason that is causing this issue in the browser?

            Many Thanks

            Image displaying notification in Outlook Desktop app

            ...

            ANSWER

            Answered 2021-Jun-03 at 20:09

            The replaceAsync method replaces a notification message that has a given key with another message. When the method completes, the callback function passed in the callback parameter is called with a single parameter of type Office.AsyncResult. But in your sample code the optional parameter (callback) is omitted. So, you will never know when it finishes.

            Source https://stackoverflow.com/questions/67823499

            QUESTION

            Reading and choosing from an Excel validation list in VBA
            Asked 2021-Jun-02 at 16:49

            I have an Excel spreadsheet - a lot of them actually - that have drop-down selections in them. I want to automate filling them in, selecting an option from the list.

            When I inspect the cell that has the drop-down in Excel itself, I cannot click on Validation in the Data Tools ribbon section as it is greyed out. I think the sheet has protection.

            When I inspect the cell in VBA, the Validation.Formula1 property contains a string like "=list_b1191f893baa0c18600db155cc008dd2_label".

            How can I find the contents of this list in VBA so that I can pick one of the valid values?

            ...

            ANSWER

            Answered 2021-Jun-02 at 16:49

            list_b1191f893baa0c18600db155cc008dd2_label would be a (presumably workbook-scoped) named range that you can pull into a Range variable like this:

            Source https://stackoverflow.com/questions/67808850

            QUESTION

            Can the Microsoft Office Ribbon be coded into a non-Office desktop application?
            Asked 2021-Jun-01 at 12:49

            Can the Microsoft Office Ribbon be coded into a non-Office Windows Forms application for VB? If so, how?

            I searched both here and on Google, but found only topics related to Office apps and add-ins, and nothing regarding non-Office use.

            ...

            ANSWER

            Answered 2021-May-31 at 20:48

            You can use the System.Windows.Controls.Ribbon.Ribbon class from the .net framework (WPF) for creating a similar UI in your applications. Office applications don't share the UI for others.

            Source https://stackoverflow.com/questions/67778525

            QUESTION

            VSTO outlook add-in - Retrieve sender's name for reply
            Asked 2021-May-27 at 03:23

            I am going through the walkthrough on how to create your first outlook addin using the ribbon designer: https://docs.microsoft.com/en-us/visualstudio/vsto/walkthrough-creating-your-first-vsto-add-in-for-outlook?view=vs-2019

            My goal is to make reply templates that includes the sender's name in the greeting.

            From researching the issue, I believe I need either MailItem.SenderEmailAddress or MailItem.Sender but when I tried to add it to the mailitem.htmlbody it doesn't show anything at all.

            Here is the code I have for my test.

            ...

            ANSWER

            Answered 2021-May-26 at 15:58

            You are accessing the sender name on the reply, not the message being replied to. The name should come from the first item in the Globals.ThisAddIn.Application.ActiveExplorer().Selection collection.

            Source https://stackoverflow.com/questions/67698052

            QUESTION

            Jhipster Spring Boot 2 instances of a microservice on different databases
            Asked 2021-May-25 at 19:18

            In my project I'm using Jhipster Spring Boot and I would like to start 2 instances of one microservise at the same time, but on different instances of a database (MongoDB).

            In this microservice I have classes, services, rests that are used for collections A, B C,.. for which now I would like to have also history collections A_history, B_history, C_history (that are structured exactly the same like A, B, C) stored in separated instance of a database. It makes no sense to me to create "really separated" microservice since I would have to copy all logic from the first one and end up with doubled code that is very hard to maintain. So, the idea is to have 2 instances of the same microservice, one for A, B, C collections stored in "MicroserviceDB" and second for A_history, B_history, C_history collections stored in "HistoryDB".

            I've tried with creating 2 profiles, but when I start from a command line History microservice, it is started ok, but if I also try to start "original" microservice at the same time, it is started but immediately history service becomes "original" microservice. Like they cannot work at the same time.

            Is this concept even possible in microservice architecture? Does anyone have an idea how to make this to work, or have some other solution for my problem?

            Thanks.

            application.yml

            ...

            ANSWER

            Answered 2021-May-20 at 09:18

            In general, this concept should be easily achievable with microservices and a suiting configuration. And yes, you should be able to use profiles to define different database connections so that you can have multiple instances running.

            I assume you are overwriting temporary build artifacts, that's why it is not working somehow. But that is hard to diagnose from distance. You might consider using Docker containers with a suiting configuration to increase isolation in this regard.

            Source https://stackoverflow.com/questions/67616962

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install Ribbon

            You can download it from GitHub.

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