dFBA | Dynamic Flux Balance analysis in Python
kandi X-RAY | dFBA Summary
kandi X-RAY | dFBA Summary
Dynamic Flux Balance analysis in Python
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- Returns the maximum y value
- Get reaction result
- Create an Extension object for the given extension
- Return a list of files in a directory
- Returns the minimum y value
- Returns the maximum number of dot products
- The minimum of the dot dot
dFBA Key Features
dFBA Examples and Code Snippets
Community Discussions
Trending Discussions on dFBA
QUESTION
I want to install a package by docker, following instruction in: https://dynamic-fba.readthedocs.io/en/latest/installation.html#installing-from-source
I installed ubuntu and then Docker. But I don't understand what I need to do next. There it is said to type (docker run -it -v ${PWD}:/opt/examples davidtourigny/dfba python3 examples/example1.py). I excatly type it in ubuntu but I get this error:
docker: Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?. See 'docker run --help'.
Using alternative method of dockerfile, I also get error. I don't know how to make use of make build, but used build instead following tutorials on the web.
It's my first time using Docker and I don't know what to do.
Any help is very appreciated.
...ANSWER
Answered 2020-Oct-14 at 05:48The Docker application has two components, a back-end server, and a front-end cli. This way you can do cool stuff like control Docker remotely or have orchestration frameworks that manage multiple Docker nodes over the network like Kubernates.
For security, the Docker back-end server is not exposed on a normal TCP port but it uses a unix domain socket (Linux magic that makes a file act as a port) at unix:///var/run/docker.sock
.
When you execute docker run -it ...
the cli application will attempt to connect to the backend server, but it looks like the daemon/server is probably not running.
Try to check that daemon is running. If you are using systemd you can check with
systemctl status docker
and start if is stopped with systemctl start docker
finally it might be good to enable it to make sure it starts automatically on reboot, you can do that with systemctl enable docker
QUESTION
I have a pandas dataframe with 1 row, I am trying to extract the values from certain columns to do calculations, error : TypeError: 'NoneType' object is not subscriptable
Failure happends where I have added - **
Code:
...ANSWER
Answered 2020-Apr-02 at 00:25This code works for me in pandas 1.0.1. Are your df columns used in your calculations numeric data types? Do you have a typo somewhere?
QUESTION
I have been able to generate the all permutation of length 4 from a string, the problem that I am facing now is that all the permutation have duplicates like {abcd) ,{adbc},{bcda}...which are all same as from Mathematical definition of set.
Is there a short version in java-8 where I can get the pure set?
My code that generated the all permutation:
...ANSWER
Answered 2020-Jan-21 at 09:44If you want to find the unique words (without considering order of characters, as you mentioned), you can do one additional step after permutation is done.
QUESTION
I'm new to AnyLogic and trying to figure out how Agent-based models should be set there. There is a famous Epidemic model, which I'm trying to reproduce. Most tutorials on classical ABM deal with old GUI settings.
For example, in version 8.5+, which is actual now, the Environment
object (that was used for positioning of layouts) has been deprecated.
Now I see that new object Canvas
is used to put the layout with agents on the page. But the structure of source code file is a bit unclear for me and I've failed to find relevant description how Canvas
can be set for the purpose. (Besides I'm not sure that this is recommended way of doing this task.)
Question: I would love to learn the right way to arbitrary position the area with agents on the page. Below you may see what I get by default.
...ANSWER
Answered 2019-Nov-15 at 05:53After some playing around, the 'minimalistic' functionality is as follows.
One should create some population with arbitrary name
Person
(population namepeople
adds automatically).The following structure of the
Project
is to be reproduced (arbitrary names are marked with yellow).
Comment: after adding a Canvas called mapCanvas
one adds the function setCanvasCellColor
with following body:
mapCanvas.fillCircle(person.getX(), person.getY(), 3, color);
It is clear that former two arguments stand for coordinates of a given point, then its size (i.e. 3) and color. Do not forget to add two arguments used in the body, namely, person
as Person
and color
as Color
.
- From Entry Action of the statechart named
state
call the just made function. I've put black color here just for the sake of demonstration;chartreuse
constant gets used instead in the Epidemic example.
main.setCanvasCellColor(this, black);
- Finally, you may run the model to get the following picture.
Note
If one is reluctant to bother with Canvas, use Main - Presentation - xxx_presentation and click Draw agent with offset to this position
checkbox.
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Install dFBA
You can use dFBA 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.
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