Jeremy Zucker

Lisp kernel request for Allegro Common Lisp

4

Hi Folks, I use [Pathway-tools](http://bioinformatics.ai.sri.com/ptools/ptools-overview.html), which uses Allegro common lisp underneath. On the other hand, if the kernel just needs to connect to a REPL through a socket, Pathway-tools already...

Supplemental: Using Gist with Jupyter notebooks

2

Hi folks, The RStudio Supplemental is nice if the workshop already includes an R lesson, but for folks who are teaching the Python lesson (especially the [Python novice Gapminder](http://swcarpentry.github.io/python-novice-gapminder/) lesson...

Use display() instead of print() to render html-formatted DataFrames

7

Hi folks, I went ahead and opened a pull request for episode 7 based on feedback from issue [#342](https://github.com/swcarpentry/python-novice-gapminder/issues/342) switching `print()` to `display()` Let me know if it displays correctly...

Use display() not print() to display a dataframe in a jupyter notebook!

16

Hi folks, I want to submit a pull request that removes all `print()` statements from the lesson, and at the very minimum, replaces them with `display()`. Jupyter notebooks by default...

Proposal: Porting R gapminder plotting episode to python with plotnine

8

Hi folks, As a software carpentry instructor, I have always been frustrated and disappointed with the current python gapminder plotting episode, especially when compared with the corresponding R gapminder plotting...

Challenge writing INDRA statements to nodelink and reading it back in to pybel

2

```python >>> import os, pybel >>> local_covid_indra_nodelink = 'covid19-indra-grounded.latest.bel.nodelink.new.json' >>> emmaa_covid_graph = pybe.from_emmaa('covid19') >>> emmaa_covid_graph.summarize() ``` ``` --------------------- ------------------------------------ Name covid19 Version d1094c2f-4b76-46b3-b317-7be29e48bb24 Author INDRA Number of Nodes 97266 Number...

to_bel_script() invokes a TypeError: make_knowledge_header() missing 1 required positional argument: 'name'

4

Hi @cthoyt When I try to run `pybel.to_bel_script()` I get the following error: ```python --------------------------------------------------------------------------- TypeError Traceback (most recent call last) in 2 3 mars_graph = get_subgraph_by_pubmed( emmaa_covid_graph, pmids) ---->...

Image('../images/2/three_nodes.png') has swapped Common Cause with Common Effect

2

Hi there, In the three_nodes.png image, for Common Cause the arrows should be pointing from $A\rightarrow B\leftarrow C$, and likewise, for Common Effect, the arrows should be pointing fr

IPOPT interface to OptLang

1

### Checklist I have an implementation of a nonlinear optimization problem for thermokinetic regulation using IPOPT, which is called through pyomo. I would like to integrate that algorithm into CobraPy,...

Added plotter argument to PhenotypicPhasePlaneResult.plot()

2

Solving issue https://github.com/biosustain/cameo/issues/288 Thanks to @jafemm for discovering this issue