bio | Bioinformatics library for .NET | Genomics library

 by   dotnetbio C# Version: Current License: Apache-2.0

kandi X-RAY | bio Summary

kandi X-RAY | bio Summary

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

.NET Bio is an open source library of common bioinformatics functions, intended to simplify the creation of life science applications. The core library implements a range of file parsers and formatters for common file types, connectors to commonly-used web services such as NCBI BLAST, and standard algorithms for the comparison and assembly of DNA, RNA and protein sequences. Sample tools and code snippets are also included.

            kandi-support Support

              bio has a low active ecosystem.
              It has 109 star(s) with 40 fork(s). There are 33 watchers for this library.
              It had no major release in the last 6 months.
              There are 14 open issues and 7 have been closed. On average issues are closed in 137 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of bio is current.

            kandi-Quality Quality

              bio has 0 bugs and 1 code smells.

            kandi-Security Security

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

            kandi-License License

              bio is licensed under the Apache-2.0 License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              bio releases are not available. You will need to build from source code and install.
              Installation instructions, examples and code snippets are available.
              bio saves you 91198 person hours of effort in developing the same functionality from scratch.
              It has 99457 lines of code, 0 functions and 908 files.
              It has low code complexity. Code complexity directly impacts maintainability of the code.

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            bio Key Features

            No Key Features are available at this moment for bio.

            bio Examples and Code Snippets

            Run a flow using a bio checkpoint .
            javadot img1Lines of Code : 12dot img1License : Permissive (MIT License)
            copy iconCopy
            public void processUsingApproachFourWithInitialCheckpoint(Flux flux) {
          "starting approach four!");
                      .checkpoint("CHECKPOINT 1", true)
            Gets the bio value .
            javadot img2Lines of Code : 3dot img2License : Permissive (MIT License)
            copy iconCopy
            public Object getBio(){
                    return bio;
            Set the bio attribute .
            javadot img3Lines of Code : 3dot img3License : Permissive (MIT License)
            copy iconCopy
            public void setBio(String bio) {
           = bio;

            Community Discussions


            How to manually insert a breakpoint that Bochs's built-in debugger will stop at? INT3 doesn't work
            Asked 2022-Feb-02 at 22:46

            I am using bochs enhanced debugger (bochs debugger with gui), but it's also debugging the BIOS code, and this is too complicated for me. So how can I set a breakpoint manually at the start of my code?

            I tried int3 but it doesn't stop on it.



            Answered 2022-Feb-02 at 12:42

            The osdev wiki describes the key features:

            Magic Breakpoint

            When you're using Bochs with the internal debugger, you can trigger the debugger via a facility called magic breakpoints. To trigger a breakpoint, you can insert xchg bx, bx (in GAS syntax, xchgw %bx, %bx) anywhere in the code and Bochs will trap into the debugger as soon as it executes it. On real hardware this has no effect as it merely replaces the BX register with itself.

            You should put the following line in your Bochs configuration file to have it listen to magic breakpoints:



            The development server returned response error code: 500 in react native when connect to firebase by installing firebase
            Asked 2022-Jan-30 at 16:20

            I try to connect to firebase by react native. Here is code



            Answered 2021-Nov-04 at 07:53

            You importing import * as firebase from 'firebase' in the top of your file..Try to import this line and tell me if it works. import firebase from "firebase/compat/app";

            Some paths of the firebase have changed a long time ago so if you are watching legacy code snipets maybe you will have errors.



            difference between %{count} and %s in validation message
            Asked 2022-Jan-26 at 14:03

            I am used to the approach below when displaying a validation message



            Answered 2022-Jan-26 at 13:49

            That s in %<...>s denotes "string". From the sprintf docs:

            For more complex formatting, Ruby supports a reference by name. %s style uses format style, but %{name} style doesn't.




            Using the CGA/EGA/VGA planar graphics modes
            Asked 2022-Jan-17 at 01:56

            I have trouble to grasp how to use colors in CGA/EGA/VGA video graphics modes. The video modes I'm particularly interested in are 0Dh (EGA 320x200) and 12h (VGA 640x480). Both of these modes have 4 planes, thus 16 colors.

            My (probably incorrect) understanding is that I should activate a set of planes by writing a bitmask to port 03C4h, then when I write to video memory, the data only gets written to the activated planes. Mostly I used this document to get my information, though I also encountered several other tutorials and discussions:

            Now I'm trying to write pixels in all possible colors in the first word in the video memory (top left part of screen). I load 1 for the initial bitmask to AH and 1 bit to BX. Then in a loop, I increment AH and shift (SHL) the bit in BX to hit a different pixel next time. I OR BX to A000h:0000h to add each pixels by leaving the already existing pixels untouched.

            What I'm expected to see is a line of pixels in all possible 16 EGA colors on the top left of the screen. What I actually see is 7 white and 1 bright yellow dots with black pixels in between them. What am I doing wrong?

            Also, every tutorial says that I must write 0005h to port 03CEh before I start to use planes. What is the purpose of that? When I comment those lines out, I can still use planes (I mean, in other programs). Previously I had success using planes when I was writing to different words in video memory (so I didn't need different color pixels in one block of 16 pixels that's represented by a single word in video memory); and when I used BIOS functions (e.g. INT 10h/AH=0Ch) to write pixels, but still I want to understand how to use planar graphics without BIOS, as I believe the BIOS functions are slow.

            Here is my code (indentation is optimized for 8-width tabs, so it kind of looks off here):



            Answered 2022-Jan-17 at 01:56

            Writing the word 0005h to ports 03CEh and 03CFh will select write mode 0. This is a complex mode that involves many features of the VGA but luckily for us most of these are reset when the video mode is set.
            However your code still needs to do the following:

            • In order to fill the VGA's internal 32-bit latch, you must perform a read-before-write operation
            • Restricting output to a single or a few pixels is done using the BitMask register.

            Next snippet displays a rainbow of 16 vertical lines that are 1 pixel wide:



            Error when using higher order function reduce
            Asked 2021-Dec-18 at 10:40

            I am working on a function that takes the total cost of all the "MP" in a value and adds it up. Here is my code for context.



            Answered 2021-Dec-18 at 02:01

            spells is a [Spell], which is shorthand for Array, and Array doesn't have a cost property. Each individual Spell in the array has its own cost property. You could say this to get an array of the spell costs and sum the costs array:



            Calling a module does not work in Raku in Windows
            Asked 2021-Dec-17 at 14:29

            I have two files main.raku and TestMod.rakumod in a directory C:\Users\suman.




            Answered 2021-Dec-08 at 07:19

            Despite what I've said in my comment, it's entirely likely that dirname is behaving according to spec; only it's not in that spec to return a platform-specific name. So it would be interesting to investigate what $*PROGRAM.dirname returns. If it's a Linux-formatted path, that might be part of the problem. This is raiph's answer points at: wrong syntax. If that's the case, we need to get to the "right" syntax. That is why in the first version of this answer I pointed at using IO::Path::Win32 to create that syntax. Other option might be to simply put the directory name by hand. Finally, a bug can't be excluded.



            SQLAlchemy - Adding a ForeignKeyConstraint to a many-to-many table that is based on another relationship
            Asked 2021-Oct-11 at 01:42

            Forgive me if this has been answered elsewhere. I've been searching SO and haven't been able to translate the seemingly relevant Q&As to my scenerio.

            I'm working on a fun personal project where I have 4 main schemas (barring relationships for now):

            • Persona (name, bio)
            • Episode (title, plot)
            • Clip (url, timestamp)
            • Image (url)

            Restrictions (Basis of Relationships):

            1. A Persona can show up in multiple episodes, as well as multiple clips and images from those episodes (but might not be in all clips/images related to an episode).
            2. An Episode can contain multiple personas, clips, and images.
            3. An Image/Clip can only be related to a single Episode, but can be related to multiple personas.
            4. If a Persona is already assigned to episode(s), then any clip/image assigned to the persona can only be from one of those episodes or (if new) must only be capable of having one of the episodes that the persona appeared in associated to the clip/image.
            5. If an Episode is already assigned persona(s), then any clip/image assigned to the episode must be related to aleast one of those personas or (if new) must only be capable of having one or more of the personas from the episode associated to the clip/image.

            I've designed the database structure like so:

            This generates the following sql:



            Answered 2021-Oct-05 at 23:19

            I can't think of any way to add this logic on the DB. Would it be acceptable to manage these constraints in your code? Like this:

            Event: a new image would be insterted in DB



            Tree data structure with multiple keys for each item
            Asked 2021-Sep-18 at 16:06

            I'm working on a chat application using node js that displays a list of online users. Each user has the following attributes:

            ipv4, rank, score, login time

            ipv4 is used when accessing a user.

            Users should be listed according to this sorting strategy:

            • Users with higher rank should be at the top of the list.
            • If the user rank is equal, the users with the highest score should be at the top of the list after high-rank users.
            • If the user score is equal, users with less login time should be at the top of the list after high-score users.

            for example:

            1. Login userA (ipv4:, rank:0, score:3000, loginTime:1631966424070)

            • list: [userA]

            2. Login userB (ipv4:, rank:1, score:2000, loginTime:1631966424080)

            • list: [userB, userA]

            3. Login userC (ipv4:, rank:1, score:1000, loginTime:1631966424090)

            • list: [userB, userC, userA]

            4. Login userD (ipv4:, rank:0, score:3000, loginTime:1631966424100)

            • list: [userB, userC, userA, userD]

            Access example:

            Get user(ipv4: -> return userC

            There are many users and I use the functional-red-black-tree data structure to improve performance. In this data structure, each item has a key and a value. The constructor of this tree takes a comparator function -like array sort comparator- with two parameters, each of which are keys, as a parameter.

            I have defined the user as follows:



            Answered 2021-Sep-18 at 16:06

            In your rand example, it is normal that the key (10, 0, 0, 0) will not match, even though ipv4=10 is somewhere in the tree. This is because that node will be more like (10, 66, 35, 19)... which will not be encountered, as the ordering of the tree is mainly based on rank, not on ipv4. The decision to where to drill down in the tree will be based on rank (0), moving to the left side of the tree, while the node you intend to find may be at the right (higher rank 66).

            What you can do is to accompany the tree with a Map, which will map an ipv4 value with an existing Key instance. So every time you insert in the tree, also add the corresponding mapping in that Map. And every time you want to find or want to delete, first retrieve the Key instance from that Map by the ipv4 value you have, and pass that Key instance to the tree's get or remove method.

            Here is a wrapper class that makes this combination. Extend it with any other method you want to include:



            Python/Selenium - how to extract text from modal fade content?
            Asked 2021-Sep-13 at 03:33

            I want to extract bios from a list of people from the website:

            I want to extract their title, company, and bio. However, bio is available only when you click each photo from the website.

            Below is my coding to extract the title & company:



            Answered 2021-Sep-13 at 03:15

            You do not have to click the images as all the modals for each speaker are fully populated in the source. You can extract the content from these modals by using driver.execute_script:



            Return outside function error eventhough it has been indented properly
            Asked 2021-Jul-10 at 11:41

            Hi I know this error is kind of silly but I am new to django. I also have indented the return function properly but it keeps on saying return outside function. I hope someone can help.

            Trace back:



            Answered 2021-Jul-10 at 11:41

            The return render(request, 'profile_page.html', {'pro': pro}) does not make much sense. A model is request unaware, and furthermore should not render any pages, that is what the views are for.

            You can return the URL where you can find the page for the UserProfile by implementing the .get_absolute_url() method [Django-doc]:


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


            No vulnerabilities reported

            Install bio

            You can download it from GitHub.


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