Compass | Silico Modeling of Metabolic Heterogeneity using Single | Genomics library

 by   YosefLab Python Version: Current License: BSD-3-Clause

kandi X-RAY | Compass Summary

kandi X-RAY | Compass Summary

Compass is a Python library typically used in Artificial Intelligence, Genomics applications. Compass 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.

In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
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              Compass has a low active ecosystem.
              It has 62 star(s) with 16 fork(s). There are 13 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 41 open issues and 36 have been closed. On average issues are closed in 21 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of Compass is current.

            kandi-Quality Quality

              Compass has no bugs reported.

            kandi-Security Security

              Compass has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              Compass is licensed under the BSD-3-Clause License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              Compass releases are not available. You will need to build from source code and install.
              Build file is available. You can build the component from source.

            Top functions reviewed by kandi - BETA

            kandi has reviewed Compass and discovered the below as its top functions. This is intended to give you an instant insight into Compass implemented functionality, and help decide if they suit your requirements.
            • Main entry function
            • Computes exchange scores for a given model
            • Compute a single sample
            • Maximize a reaction
            • Make unidirectional reactions
            • Invert the molecule
            • Generic parallel map function
            • Parallel map function
            • Computes a Compassposed Compression problem
            • Get the list of reactions
            • Limit exchange reactions
            • Compute NearestNeighbors
            • Compute stochastic constraints
            • Returns a dictionary of the SMAT term as a dictionary
            • Get the maximum flux
            Get all kandi verified functions for this library.

            Compass Key Features

            No Key Features are available at this moment for Compass.

            Compass Examples and Code Snippets

            No Code Snippets are available at this moment for Compass.

            Community Discussions

            QUESTION

            Comparing Week of Year with "overflow"
            Asked 2021-Jun-15 at 20:49

            So I want to be able to look at a specific week of the year and look at all data in the preceding and following 6 weeks.

            WHERE t1.weeknum >= week-6 AND t1.weeknum <=week+6

            So if week is 20, I want to return everything between 14 and 26.

            The problem is weeks >=47 and <=6. For instance, if week is 4, I want the range to be 50 through 10. Years are a separate dimension and I am including all data regardless of year.

            I think this would be similar to a compass heading. Say you are at 350 degrees and turn right 30 degrees. 350+30 = 20 degree bearing.

            I'm using SQL Server Express

            ...

            ANSWER

            Answered 2021-Jun-15 at 20:11

            The Modulus operator (%) seems to be what you want. Since you are using the range 1 to 52 to represent week numbers you need to shift the range to 0 to 51 while calculating:

            Source https://stackoverflow.com/questions/67990100

            QUESTION

            how to connect to mongodb server via ssh tunnel with Proxy Jump (Bastion Host)
            Asked 2021-Jun-11 at 04:04

            I have an ssh config file like this. I have a proxy jump to host1 from test2.

            ...

            ANSWER

            Answered 2021-Jun-11 at 04:04

            I am able to connect to the database now.

            1. Make a tunnel through Bastion to the Database from the terminal.

              ssh -L 27017:{mongodb-host}:27017 host1

            2. I am able to connect to database via the tunnel from localhost in another terminal.

              mongo --host 127.0.0.1:27017 --username {username} --password {password}

            So I am able to connect through mongoose too using connection string. mongodb://dbadmin:{username}:{password}@localhost:27017

            Source https://stackoverflow.com/questions/67747533

            QUESTION

            Encoding issue when performing aggregation to find average by group in pymongo
            Asked 2021-Jun-07 at 07:36

            I have a dataset of items inside an orders collection:

            ...

            ANSWER

            Answered 2021-Jun-07 at 07:36

            You have extra braces around "$total"; try:

            Source https://stackoverflow.com/questions/67865300

            QUESTION

            implement crossroads logic in prolog
            Asked 2021-Jun-06 at 06:47

            I want to write a programm, that checks if a car is allowed to drive/turn on a crossroads. The cars are identified by colors (e.g. blue, grey, red), the positions of the cars are defined by compass direction (north, east, south, west). the function to check if allowed to drive is allow(Color). (e.g. allow(blue).)

            This is my actual code:

            ...

            ANSWER

            Answered 2021-Jun-06 at 06:47

            Your comments pretty much hint the problem. You define a car to be alĺowed if it can either go right, go left, or go straight.

            In case of allow(red) and allow(grey) all of these options are checked, all of them are wrong, thus false is printed immediately.

            In case of allow(blue), the first option is checked first and it evaluates to true, which is printed. However, this time Prolog knows that there are options that are not checked yet and waits for you to request further computation.

            Prolog then checks the second two options, which evaluate to false because the blue car neither wants to go left nor straight.

            Since Prolog can't know that every car only ever has one directional wish, it cannot abort the computation after the first result because in other circumstances, additional solutions are required.

            There are two easy way to fix this:

            • Use the cut-goal (!) after each option. Please be aware that this might change the semantics (compare red vs. green cut in the link). In your case it's a red cut because it changes the semantics.

            Source https://stackoverflow.com/questions/67840882

            QUESTION

            Unown Way To Change Parameter Inside Mongoose
            Asked 2021-Jun-05 at 06:30

            I am having some issues with saving an object parameter into a mongoose map. My collection looks like this. The collection's name is guildtickets:

            ...

            ANSWER

            Answered 2021-Jun-05 at 06:30

            QUESTION

            Distinguish similar RGB pixels from noisey background?
            Asked 2021-Jun-04 at 08:45

            Context: I am trying to find the directional heading from a small image of a compass. Directional heading meaning if the red (north) point is 90 degrees counter-clockwise from the top, the viewer is facing East, 180 degrees is south, 270 is west, 0 is north. etc. I understand there are limitations with such a small blurry image but I'd like to be as accurate as possible. The compass is overlaid on street view imagery meaning the background is noisy and unpredictable.

            The first strategy I thought of was to find the red pixel that is furthest away from the center and calculate the directional heading from that. The math is simple enough.

            The tough part for me is differentiating the red pixels from everything else. Especially because almost any color could be in the background.

            My first thought was to black out the completely transparent parts to eliminate the everything but the white transparent ring and the tips of the compass.

            True Compass Values: 35.9901, 84.8366, 104.4101

            These values are taken from the source code.

            I then used this solution to find the closest RGB value to a user given list of colors. After calibrating the list of colors I was able to create a list that found some of the compass's inner most pixels. This yielded the correct result within +/- 3 degrees. However, when I tried altering the list to include every pixel of the red compass tip, there would be background pixels that would be registered as "red" and therefore mess up the calculation.

            I have manually found the end of the tip using this tool and the result always ends up within +/- 1 degree ( .5 in most cases ) so I hope this should be possible

            The original RGB value of the red in the compass is (184, 42, 42) and (204, 47, 48) but the images are from screenshots of a video which results in the tip/edge pixels being blurred and blackish/greyish.

            Is there a better way of going about this than the closest_color() method? If so, what, if not, how can I calibrate a list of colors that will work?

            ...

            ANSWER

            Answered 2021-Jun-04 at 08:45

            If you don't have hard time constraints (e.g. live detection from video), and willing to switch to NumPy, OpenCV, and scikit-image, you might use template matching. You can derive quite a good template (and mask) from the image of the needle you provided. In some loop, you'll iterate angles from 0° to 360° with a desired resolution – the finer the longer takes the whole procedure – and perform the template matching. For each angle, you save the value of the best match, and finally search for the best score over all angles.

            That'd be my code:

            Source https://stackoverflow.com/questions/67829092

            QUESTION

            MongoDB: Arrays size with $where - ReferenceError
            Asked 2021-Jun-01 at 16:18

            For MongoDB 4.4.6

            For a collection with an array - If I use

            ...

            ANSWER

            Answered 2021-Jun-01 at 16:18

            You can use $expr operator to use aggregation operator $gte and $size,

            Aggregation Alternatives Preferred
            Starting in MongoDB 3.6, the $expr operator allows the use of aggregation expressions within the query language.

            Source https://stackoverflow.com/questions/67791958

            QUESTION

            How can I add a new field from another one value?
            Asked 2021-May-27 at 17:16

            I have a collection "people" with documents like this one:

            ...

            ANSWER

            Answered 2021-May-27 at 17:12

            QUESTION

            Mongoose failing with $in: [number array]
            Asked 2021-May-24 at 20:56

            MongoDb documents looks like this:

            ...

            ANSWER

            Answered 2021-May-24 at 20:56

            QUESTION

            MongoDB Aggregation "group" with "max" field within a sub-array
            Asked 2021-May-23 at 14:42

            Using Compass initially, I then need to convert it into the PHP library.

            So far, I have a 1st stage that filters the documents on 2 fields using $match:

            • comp.id (sub-document / array)
            • playerId

            Code is: $match (from drop-down)

            ...

            ANSWER

            Answered 2021-May-23 at 06:11
            • $match your conditions
            • $unwind deconstruct holes array
            • $sort by nettPoints in descending order
            • $group by no and select first holes object

            Source https://stackoverflow.com/questions/67654067

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

            Vulnerabilities

            No vulnerabilities reported

            Install Compass

            You can download it from GitHub.
            You can use Compass 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://github.com/YosefLab/Compass.git

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            gh repo clone YosefLab/Compass

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            git@github.com:YosefLab/Compass.git

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