Useful Links Collection by Amanda from Griffith Hacky Hour

Amanda Miotto from Griffith Hacky Hour  has collected together a great set of links that she often uses or refers people to at the Hacky Hours her and her team run. Thanks for sharing Amanda!

 

Bioinfo

Bioinformatics Tutorials | Phil Chapman’s Blog
Nature in Code by Marcel Salathé [Leanpub PDF/iPad/Kindle]
QFAB members’ clinics in bioinformatics, biostatistics and biodata | QFAB BIOINFORMATICS
ROSALIND | learn BioInfo
Degust

 

Chem

Marvin JS – v17.22.0

 

Data Science

[Discuss] Programming language by research discipline
Becoming a Data Scientist – Curriculum via Metromap ← Pragmatic Perspectives
Data Intro for Librarians: Introduction to Data
daattali/addinslist: Discover and install useful RStudio addins
DataCamp: Learn R, Python & Data Science Online
early beginner | Difficulty Levels | Data Sci Guide
Exploratory Data Analysis Course Notes
Getting Started with swirlify
Home Page | CyVerse
Python vs. R: The battle for data scientist mind share | InfoWorld
PythonDataSciHandbookJupyter
R Data Import/Export
swirldev/swirl_courses: A collection of interactive courses for the swirl R package.
Tamara Munzner: Talks
The Architecture of Open Source Applications: VisTrails
Videos | VIZBI
Design with Intent | Insights, methods and patterns for designing with people, behaviour and understanding
Chart.js | Open source HTML5 Charts for your website
Recommended Resources for Beginners | Data Sci Guide
Image processing in Python — scikit-image

 

Data Vis

Knight Lab
Search for Charts by Data Visualization Functions
visgap.pdf

 

Dir of Tools and Repos

Browse by subject | re3data.org
Copy of 400+ Tools and innovations in scholarly communication – Google Sheets
Course Resources | Intersect Australia Limited
Datasets | Kaggle
openscience.org/links/
Research Tools | UTS Library – University of Technology, Sydney
Welcome // | DiRT Directory
Welcome // | DiRT Directory
Optical character recognition – Wikipedia
Open Knowledge Maps – A visual interface to the world’s scientific knowledge
Science
Open Knowledge: Projects
The Open Data Handbook
ckan – The open source data portal software
Coding Resources | Women Who Code

 

Eco

Free and Open Access to Biodiversity Data | GBIF.org
SunPy
What is Dr Climate? | Dr Climate
ZoaTrack – Free Animal Tracking Software
Education | DataONE
Macroeco: Ecological pattern analysis in Python — macroeco 1.0 documentation

 

File Reshaping

CSVshare
Tabula: Extract Tables from PDFs
Whiteboard Picture Cleaner – Shell one-liner/script to clean up and beautify photos of whiteboards!

 

Geo

Geospatial data and metadata – ANDS
Getting Started

 

Git & Tech Writing

Contribute to someone’s repository
Front matter · GitBook
github free programming books
HackMD – Collaborative markdown notes
The Journal of Open Source Software
Who is this for? · GitBook
Github for the useR
Git Flow
On undoing, fixing, or removing commits in git
GitHub for Beginners | GitHub Resources Library
GitHub Guides
Git Tutorial – Try Git

 

HASS

All Those Shapes — Google Arts & Culture
Data Visualization for Social Science
Discursis :: About
Google Arts & Culture
Google Expeditions
Humanities Networked Infrastructure – HuNI
Omeka
Word Tree / Fernanda Viegas & Martin Wattenberg
2018 DMRC Summer School – Workshops – Digital Media Research Centre

 

HPC

Gnu Parallel – Parallelize Serial Command Line Programs Without Changing Them
HPC in a day
HPC in a day
HPC in a day: Logging In
Nectar training
Training Material – User Support Documentation – Pawsey Documentation
Training – National Computational Infrastructure
QRIScloud Documentation
HPC self-help and support – University of Southern Queensland
USQ HPC cheatsheet
Pawsey Online Course: Developing Parallel Codes with MPI :: The Pawsey Supercomputing Centre
Pawsey Online Course: GPU Training Essentials :: The Pawsey Supercomputing Centre

 

IT Misc

Atom
Code Carabiners: Essential Protection Tools for Safe Programming – O’Reilly Radar
Code for a Living – Stack Overflow Blog
Episodes – [Talk Python To Me Podcast]
How To Get Started With The Ubuntu Linux Distro | Gizmodo Australia
jakevdp/WhirlwindTourOfPython: The Jupyter Notebooks behind my OReilly report, “A Whirlwind Tour of Python”
Research Computing | File Transfers with FileZilla | ResearchIT
The Unix Workbench
Weka 3 – Data Mining with Open Source Machine Learning Software in Java
Hard Coding Concepts Explained with Simple Real-life Analogies
R for Excel users – Rex Analytics
Rex Blogs – Rex Analytics
Torfs+Brauer-Short-R-Intro.pdf
CodeNewbie
GNU Parallel tutorial
Web designing tutorial list
one.
 

Cheatsheets

MiscCheatsheets

 

Lessons and Books Misc

Free Courses Online | Open2Study
Subjects – OpenStax
Greg Wilson | DataCamp
Browse Online Courses – FutureLearn
 

Math

Science:Math Exam Resources – UBC Wiki

 

Misc Cool

Calling Bullshit — Syllabus

 

Stats Help

5minuteStats
Cross Validated
Which Stats Test – SAGE Research Methods

Altmetric- social media tracking PublicationsAsk the ODI Australian NetworkCoffee with Recovering Academics – Beth M. Duckles – MediumInsights – Stack Overflow BlogLabs and Tools – NectarMonthly Tech Talk Pages – Monthly Tech Talk (Melbourne) | MeetupOpenWetWarePLOS Collections: Article collections published by the Public Library of ScienceScience Hack Day BrisbaneZooniverse

 

For Coordinators

Explore Erudite – BD2K Training Coordinating Center
mozilla-studygroup-leads-may-2017 | Etherpad
Outline of academic disciplines – Wikipedia
Repeat After Me – by Maki Naro
The Carpentries Community Cookbook documentation
Carpentries Handbook — Carpentries Handbook documentation

Tinkercad | Create 3D digital designs with online CADAbout – data.gov.au

SoftwareCarpentrySetup

Submissions
Configuration Problems and Solutions · swcarpentry/workshop-template Wiki

Image analysis for biologistsSecure storage – digital dataCloud Genomics

 

13 problem owners and helpers this week

Busy week with questions on R, C++, data viz, Python, machine learning and sparse matrix representations. Five new faces with questions to ask. And great to see so many helpful helpers donating their time.

Who is a helper and who has questions?

hacky_hour-2017-05-23-Jess_Steffen

This week Jess who was writing a macro in ImageJ, and Steffen who had a question on compiling HPC code but was also helping Jess. It’s great when our Hacky Hourers help each other!

hacky_hour-2017-05-23-Emily_James-small

Also, Emily, who wanted to code some maximum likelihood estimations in R, here with our regular resident R expert, James.

Find us

It’s easy to find us at the regular Tuesday 3pm at Nano’s Cafe UQ Hacky Hour. Just look for the sign.

hacky_hour_sign

This week at Hacky Hour …

This week at Hacky Hour UQ, newbie Danni who wants to script HPC jobs & regular Iva who’s having trouble with C compilers. Felicity (not shown) who is doing a digital librarian residency in Faculty of HASS popped in to provide library/data management advice.

hacky_hour-2017_04_17-1-small

Finding your Hacky Hour helpers

Not sure how to find the Hacky Hour gang at Nano cafe on Tuesdays at 3 o’clock? We have just made it easier. Some of us will be wearing the new Hacky Hour T shirt and drinking from our new Hacky Hour mugs. Get a sticker to take away too.

So much Hacky Hour action today

Cam Allen’s visit to Hacky Hour today was a big success. Lots of people turned out to meet Cam and to hear more about how the Zooniverse can help with crowd-sourced science. Projects discussed ranged from eco sounds to bird identification through to bioinformatics. The Zooniverse has supported some amazing projects, from Shakespeare’s World and Amazon Aerobotany to stargazing and planet watching in many of the astronomical projects.

Another project, Planet 9, is the focus of the BBC’s Stargazing Live. The ABC’s Stargazing Live, with Brian Cox, and supported by the Zooniverse, starts on local TV tonight and runs for three nights.


Great to have a drop-in from Amanda Miotto, one of Griffith University’s Hacky Hour wranglers, talking here with Jake Parker.