Medusa | Analysis of ensembles of metabolic network reconstructions

 by   opencobra Python Version: v0.2.1 License: MIT

kandi X-RAY | Medusa Summary

kandi X-RAY | Medusa Summary

Medusa is a Python library. Medusa has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

Analysis of ensembles of metabolic network reconstructions
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            kandi-support Support

              Medusa has a low active ecosystem.
              It has 16 star(s) with 8 fork(s). There are 4 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 25 open issues and 15 have been closed. On average issues are closed in 109 days. There are 9 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of Medusa is v0.2.1

            kandi-Quality Quality

              Medusa has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              Medusa 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

              Medusa releases are available to install and integrate.
              Build file is available. You can build the component from source.
              Medusa saves you 580 person hours of effort in developing the same functionality from scratch.
              It has 1354 lines of code, 57 functions and 23 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed Medusa and discovered the below as its top functions. This is intended to give you an instant insight into Medusa implemented functionality, and help decide if they suit your requirements.
            • Iterative gapfill from binary phenotypes
            • Calculate the gapfill solution for the given model
            • Builds an ensemble from gapfill solutions
            • Calculate the gap - fill algorithm
            • Validate the model
            • Returns the state of the given member
            • Performs a single gene deletion operation
            • Set the state of a specific member
            • Test whether a model is leak
            • Optimizes an ensemble
            • Constructs an ensemble of gap - fill solutions
            • Performs a single reaction deletion
            • Populates members from a list of models
            • Optimize the ensemble worker
            Get all kandi verified functions for this library.

            Medusa Key Features

            No Key Features are available at this moment for Medusa.

            Medusa Examples and Code Snippets

            No Code Snippets are available at this moment for Medusa.

            Community Discussions

            QUESTION

            git-filter-repo multiple operations (regex filter, move files, keep other dir...)
            Asked 2022-Jan-15 at 15:22

            I'm trying to filter a repository with git-filter-repo. I was trying to do this by describing all my needed operations in a path file to be used in a --paths-from-file stanza as described in the documentation but I'm stuck in a last step to finalize this in one single and easy step.

            Situation and expected result

            My git working directory looks like this:

            ...

            ANSWER

            Answered 2022-Jan-15 at 15:22

            Self answering as laying out the problem helped me spot the issue. I missed one important note in the documentation about path renaming.

            Note: if you combine path filtering with path renaming, be aware that a rename directive does not select paths, it only says how to rename paths that are selected with the filters.

            So one must describe all paths to be selected in the original repo prior to renaming them. Hence in my case the regex must be defined twice: once as a simple path filter and the other as a rename. The following path file is perfectly doing the job in a single run:

            Source https://stackoverflow.com/questions/70720401

            QUESTION

            Pandas compare all values of a column with different DataFrame and return column name (of a dif. DataFrame) where value matches
            Asked 2022-Jan-07 at 20:01

            I'm trying to assign category per row of a dataset based on matching keywords from other dataset.

            1. I compare df_ONE['columnname'] to every value of df_TWO
            2. and if matching value found use column name of df_TWO where this value is located as a cell value of new column in df_ONE.

            With example below, all the values of a new string would be non-sport (column name of df_TWO where the value is found)

            df_ONE

            ...

            ANSWER

            Answered 2022-Jan-07 at 20:01

            You need to reshape your second dataframe. You can do this with melt pretty easily.

            Here is an example of what the melted df looks like:

            Source https://stackoverflow.com/questions/70626440

            QUESTION

            K8ssandra deployment "Error connecting to Node (endPoint=/tmp/cassandra.sock)"
            Asked 2022-Jan-05 at 01:25

            I'm trying to run K8ssandra but the Cassandra container keeps failing with the following message (Repeating over and over):

            ...

            ANSWER

            Answered 2022-Jan-05 at 01:25

            I was able to fix this by increasing the memory to 12Gi

            Source https://stackoverflow.com/questions/70537865

            QUESTION

            How can I randomly assign powers to my heroes?
            Asked 2021-Dec-22 at 00:39

            I'm creating a hero game. I've created a dictionary containing magic powers, my problem is how can I create a method that will randomly assign 12 magic powers to 4 of my heroes (each hero get's 3 powers) without one magic power being assigned multiple times? Here's my code:

            ...

            ANSWER

            Answered 2021-Dec-22 at 00:39

            This goes through the set of 12, and if you ask for more, it will reshuffle them again.

            Source https://stackoverflow.com/questions/70443074

            QUESTION

            Filter/Map JSON in React to products
            Asked 2021-Nov-29 at 05:33

            i have this Json file, it was created by me so if I would have to do some restructuring, it will be welcome.

            ...

            ANSWER

            Answered 2021-Nov-27 at 19:42

            First you should get your array of categories you need to show. Then based on this array of categories we can show data. So it can be like this:

            Source https://stackoverflow.com/questions/70137601

            QUESTION

            Is it possible to backup and restore Cassandra cluster using dsbulk?
            Asked 2021-Sep-28 at 17:33

            I searched through the internet a lot and saw a lot of ways to backup and restore a Cassandra cluster, such as nodetool snapshot and Medusa. but my question is that can I use dsbulk to backup a Cassandra cluster. What are its limitations? Why doesn't anyone suggest that?

            ...

            ANSWER

            Answered 2021-Sep-28 at 17:33

            It's possible to use it in some cases, but it's not practical because (that are primary, list could be bigger):

            • DSBulk put an additional load onto the cluster nodes because it's going through the standard read path. In contrast to that nodetool snapshot just create a hardlinks to the files with data, no additional load to the nodes
            • It's harder to implement incremental backups with DSBulk - you need to come with condition for SELECT that will find only data that changed since the last backup, so you need to have timestamp column, because you can't do the WHERE condition on the value of writetime function. Plus it will require rescanning of whole data anyway. Plus it's impossible to find what data were deleted. With nodetool snapshot, you just compare what files has changed since last backup, and backup only them.

            Source https://stackoverflow.com/questions/69364605

            QUESTION

            Why do I get this error when I'm trying to create models from database?
            Asked 2021-May-05 at 06:07

            I'm trying to create models from my Oracle database 10g using Entity Framework Core 5 dbcontext scaffold:

            ...

            ANSWER

            Answered 2021-May-05 at 06:07

            The fine manual says minimum oracle 11.2 for that provider

            Upgrade your db or change provider

            Source https://stackoverflow.com/questions/67395767

            QUESTION

            Logback in a Java modular application not working
            Asked 2021-Apr-14 at 15:43

            I am just starting to master modular applications and I have a problem with the logback.

            Before modularity was introduced into the project, Logback successfully worked with the same settings.

            As soon as I start working with the LoggerContext and add the line requires ch.qos.logback.classic to the module-info.java, the application crashes.

            Crash occurs in the line receiving the logger:

            ...

            ANSWER

            Answered 2021-Apr-14 at 14:28

            QUESTION

            How to read file into class in C++?
            Asked 2021-Apr-12 at 17:05

            I am reading File that contains

            ...

            ANSWER

            Answered 2021-Apr-12 at 17:05

            This code reads your file and stores the data in the std::vector Info using stringstreams and other things to parse.

            Source https://stackoverflow.com/questions/67061682

            QUESTION

            Error when trying to retrieve from database
            Asked 2021-Feb-17 at 13:04

            I have generated three classes from XSD schema:

            ...

            ANSWER

            Answered 2021-Feb-17 at 12:50

            We are missing the medusa initialization code, but you should do something like this:

            Source https://stackoverflow.com/questions/66242165

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

            Vulnerabilities

            No vulnerabilities reported

            Install Medusa

            You can download it from GitHub.
            You can use Medusa like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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          • HTTPS

            https://github.com/opencobra/Medusa.git

          • CLI

            gh repo clone opencobra/Medusa

          • sshUrl

            git@github.com:opencobra/Medusa.git

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