KAMI | Bio-curation library for modelling cellular signalling | Graph Database library
kandi X-RAY | KAMI Summary
kandi X-RAY | KAMI Summary
The platform allows to input annotated biological facts through the graphical interface or pro- grammatically through the API. The input facts can be automatically merged with an existing model in a context-dependent manner (the knowledge present in the model influences the way these facts are interpreted and, therefore, merged with the model). The model itself is a graph hierarchy (an instance of ReGraph’s core data structure). Apart from the user input knowledge, the hierarchy con- tains expert knowledge used by KAMI for the interpretation of interactions, for example, definitions of protein families, protein variants definitions, the semantics of particular protein domains. This expert knowledge is obtained from both publicly available data (such as UniProt, Pfam, InterPro databases) and from collaboration with biologists. From the knowledge aggregated by a user in the hierarchy, KAMI allows to automatically instantiate models expressed with Kappa rules and perform simulations with KaSim.
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Top functions reviewed by kandi - BETA
- Export a Kami model hierarchy
- Find the label for a given node
- Find the gene in the given actor list
- Create rule declaration
- Merge fragments
- Compute the overlap between two files
- Check if two fragments are the same
- Folds a nugget
- Return a mapping of components to agents of the given component
- Generate a set of site bnd sites
- Given a list of InterPro IDs return the proposed name and label
- Remove conflict between two nodes
- Add a state to the action graph
- Generate the kami s sites
- Prints summary of the AGENT ANATOMY
- Add a site to the action graph
- Adds a region to the action graph
- Create an instance from the given json data
- Generates the instantiation rules from a json_context
- Create a new model
- Expand a locus into a single gene
- Compose a list of splices
- Creates a layout for each gene
- Get a subgraph from the hierarchy
- Merge overlapping fragments
- Adds a residue to the action graph
KAMI Key Features
KAMI Examples and Code Snippets
Community Discussions
Trending Discussions on KAMI
QUESTION
I have list of article, title, and keyword contains this word:
...ANSWER
Answered 2021-Apr-14 at 08:18It's a bit unclear to me what you are trying to achieve, but the way I interpret the question is that you want to iterate over the articles in article, check if any of the keywords appear in the article and append those keywords to ab, or, if none of the keywords appear in the article, extend ab with any keywords that appear in the corresponding title of the article. If this is the correct interpretation, then you could do something like this:
QUESTION
I am trying to find out the most popular job position employees are working at a combination of companies. If there is a tie, however, then both are added to the table.
I have a file called employees_data.txt. I have their name, company, job position, and age in that order.
...ANSWER
Answered 2021-Apr-08 at 00:04Feels like homework :laugh:
You need an aggregate (count, sum, min,max, etc,.) and a group by
QUESTION
I'm accessing ncdf files directly from a website [here][1] into my RMarkdown. When I try to read the file using the nc_open functions as in the code below, I get the error 'Passed a filename that is NOT a string of characters!' Any idea how I can solve this? ps: I even tried uncompressing the files with the gzcon function but the result is the same when I try to read the data. Thanks for your help! Kami
...ANSWER
Answered 2021-Apr-04 at 15:56Is this a mode="w" Vs mode="wb" issue. I've had this with files before. No experience of ncdf4.
Not sure if you can pass mode="wb" to get but does
file.download(yourUrl, mode="wb")
Work / help
Edit:
Ah. Other thing is you are storing the object as an object (nc) but nc_open wants to open a file.
I think you need to save the object locally (unless nc_open can just take the URL) and then open it? Possibly after unzipping.
QUESTION
Whenever I try to login or signup (both actions that lookup in my database) I get a weird "NotImplementedError: built-in function getitem" error from my backend and it returns 500.
The code was working earlier today and I cannot for the life of me find out what changed that broke it. My db has a simple structure : users and roles and association between them. I can commit things into my db just fine using something like this :
...ANSWER
Answered 2021-Apr-07 at 19:16Answer was using Flask-User instead of Flask-RBAC for roles, as the latter is crappy and I can't get it to work.
QUESTION
I have seen the post in here : https://github.com/tidyverse/dplyr/issues/3101 and tried to work with summarise_at, however it doesn't work with 3 functions, instead I found simpler with summarise_all. Is there any way to reduce the inner join from my code?
...ANSWER
Answered 2021-Mar-03 at 23:53You ca use across() to apply a summarizing function to a set of columns
QUESTION
I have this spider in scrapy
...ANSWER
Answered 2021-Feb-01 at 03:23OLD VERSION:
At this moment I found only .re(".+") to get all (more or less) as list
QUESTION
i got this error when i'm trying to send multiple email, and i also want to pass a data to mail view.
here is my controller:
...ANSWER
Answered 2021-Jan-14 at 10:47You don't need to wrap the result of your query in an array. Also if you only want the email field from these records you could use pluck to get a list of them:
QUESTION
so i made a list and i used tkinter for choosing a random data in list and showing that in a showinfo box. now i was just wondering if its possible to make a random image for random data. for eg i am making a app that generates a random anime name from the list but i want to add the anime picture also is there any way i can do that ? i haven't tried building it but here is what i have made so far.
i have no error i just want to have different picture for different names from the list chose randomly
...ANSWER
Answered 2021-Jan-14 at 09:26Since you want the image to be corresponding to the anime titles I suggest you use a dictionary instead of a list. Also, use Toplevel widget to display the output.
So here is an example code:
QUESTION
So I have exported result from scraping news portal which I stored it to DataFrame, then I export it to csv and json. The scraping, export to csv got no problem, and technically got no problem export it to json too. Here is the result in json files:
ANSWER
Answered 2020-Nov-24 at 15:59Get current time
QUESTION
A small sample of the columns are as follows:
...ANSWER
Answered 2020-Nov-23 at 15:13Try this approach. It uses a join after reshaping data by id and name. Also, some cleaning tasks were needed as names had spaces and lower, upper cases. Here the code using dplyr and tidyr:
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install KAMI
You can use KAMI 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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