GenevieveBuckley

# Proposed slices_from_chunks_overlap function 
# Mofified from slices_from_chunks from dask.array.core
from itertools import product
from dask.array.slicing import cached_cumsum


def slices_from_chunks_overlap(chunks, array_shape, depth=1):
    """Translate chunks tuple to a set of slices in product order
    Parameters
    ----------

GenevieveBuckley

conda install -c conda-forge/label/cupy_rc cudatoolkit=11.2 cupy=9.0.0b3

GenevieveBuckley

TITLE:

Scaling Science: leveraging Dask for life sciences

SHORT ABSTRACT:

Managing the challenges associated with big data in life sciences can be difficult. Scalable scientific computing is required to cope with the increasing demands of modern biology and neuroscience. Dask is a python library for distributed computation. In this talk, we'll look at several case studies where Dask is used to scale up data processing for life sciences. It will include examples from statistical genetics, single cell analysis, and imaging visualization & analysis. This will give you a better understanding of how you can extend code with Dask to scale your analysis.

DESCRIPTION:

GenevieveBuckley

name: cellprofiler-dev
channels:
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=1_gnu
  - alsa-lib=1.2.3=h516909a_0
  - atk-1.0=2.36.0=h3371d22_4
  - brotlipy=0.7.0=py38h497a2fe_1001

GenevieveBuckley

CellProfiler development installation on Ubuntu 20.04

Guide created February 2021

1. Install dependencies

Install these dependencies

sudo apt update
sudo apt -y upgrade
sudo apt install -y make gcc build-essential libgtk-3-dev
sudo apt-get install -y python3-pip openjdk-11-jdk-headless default-libmysqlclient-dev libnotify-dev libsdl2-dev

GenevieveBuckley

GenevieveBuckley

Example images used can be downloaded from here: https://github.com/DeMarcoLab/correlateim/tree/master/data

GenevieveBuckley

#!/usr/bin/env python3

"""
quicky script that compares two conda environments

can be handy for debugging differences between two environments

This could be made much cleaner and more flexible -- but it does the job.

Please let me know if you extend or improve it.

GenevieveBuckley

# From https://coderwall.com/p/-wbo5q/pip-install-a-specific-github-repo-tag-or-branch
pip install -e git://github.com/{ username }/{ reponame }.git@{ tag name }#egg={ desired egg name }

GenevieveBuckley

briefcase android project

phone MUST be in file transfer mode
Must wait for the computer to recognise that the phone has been plugged in
Must allow USB debugging

https://pastebin.com/0xpejQPB

Traceback (most recent call last):
  File "/home/xero/.virtualenvs/beeware-venv/bin/briefcase", line 8, in <module>