Zsailer

Sub-teams

Here is a list of proposed sub-groups to give anouncements each meeting:

1. Jupyter Core
2. Jupyter Lab
3. nteract
4. Jupyterhub
5. Binder
6. IPython Core

Zsailer

Open and reproducible science

(powered by Jupyter)

Link to Open Science Collaboration:

http://science.sciencemag.org/content/349/6251/aac4716

How to practice open and reproducible research

Zsailer

import phylovega as phy




tree = phy.Tree(data).encode(
    nodes=[],
    edges=[],
    node_color=[],
    edge_color=[],

Zsailer

Create conda environment.

conda create -n <kernel name> pip jupyter 

Activate environment.

source activate <kernel name>

Zsailer

Zsailer

import pandas as pd
import pandas_flavor as pf

@pf.registor_dataframe_method
def check_columns(df):
    # Required columns
    required_cols = {'x', 'y', 'z'}

    # Find columns missing from 
    if required_cols.issubset(df.columns) is False:

Zsailer

from IPython.display import HTML
from IPython.display import display

# Taken from https://stackoverflow.com/questions/31517194/how-to-hide-one-specific-cell-input-or-output-in-ipython-notebook
tag = HTML('''<script>
code_show=true; 
function code_toggle() {
    if (code_show){
        $('div.cell.code_cell.rendered.selected div.input').hide();
    } else {

Zsailer

Towards defining a (phylogenetic) tree JSON Format

After a fair bit of digging, I was unable to find a single, defined JSON structure for phylogenetic data. With awesome visualization libraries (like D3) emerging, I think it is necessary to standardize a JSON grammar to allow libraries like DendroPy to access such visualizations.

In this document, I attempt to define this set of rules and grammar.

Metadata Keys

Zsailer

Dendropy's Tree class to JSON format

A proposed JSON format for Dendropy's Tree class. This is D3 inspired, and easily portable to all of D3's hierarchical visualization examples.

Example

For the following example, I'll use the simple string (taken from wikipedia) converted to a JSON format

(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;  

Zsailer

# By Jake VanderPlas
# License: BSD-style

import matplotlib.pyplot as plt
import numpy as np


def discrete_cmap(N, base_cmap=None):
    """Create an N-bin discrete colormap from the specified input map"""