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Genevieve Buckley GenevieveBuckley

  • Monash University
  • Melbourne
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@GenevieveBuckley
GenevieveBuckley / Dask-task-graph-handling-costs-on-the-client.ipynb
Last active June 1, 2021 06:49
Dask task graph handling costs on the client
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GenevieveBuckley / distributed-skeleton-analysis.ipynb
Last active May 6, 2021 10:04
distributed skeleton analysis
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GenevieveBuckley / slices_from_chunks_overlap.py
Last active November 10, 2021 00:29
slices_from_chunks_overlap
# 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
----------
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GenevieveBuckley / install_cupy_9.0.0b3.txt
Created March 15, 2021 07:47
How to install the beta version of Cupy 9.0.0
conda install -c conda-forge/label/cupy_rc cudatoolkit=11.2 cupy=9.0.0b3
@GenevieveBuckley
GenevieveBuckley / talk_proposal_scipy_2021.md
Last active May 11, 2021 04:02
Talk proposal SciPy 2021

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:

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GenevieveBuckley / cellprofiler-environment-dev-ubuntu-20-04.yml
Created February 11, 2021 02:35
CellProfiler development conda environment export
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
GenevieveBuckley / cellprofiler-dev-installation-ubuntu-20-04.md
Last active February 11, 2021 02:33
CellProfiler development installation on Ubuntu 20.04

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 / restart-and-run-all.ipynb
Created November 10, 2020 22:40
Jupyter notebook restart and run all
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GenevieveBuckley / example-images.txt
Last active October 8, 2020 07:09
worm demo for napari affine transforms
Example images used can be downloaded from here: https://github.com/DeMarcoLab/correlateim/tree/master/data
#!/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.