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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
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
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
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
Lessons and Books Misc
- Free Courses Online | Open2Study
- Subjects – OpenStax
- Greg Wilson | DataCamp
- Browse Online Courses – FutureLearn
-
Math
Misc Cool
Stats Help
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
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.
Steven, Catherine and Steffen
Jenny and Anne
Liam and James
Who is a helper and who has questions?
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!
Also, Emily, who wanted to code some maximum likelihood estimations in R, here with our regular resident R expert, James.
This week, single cell sequence analysis in R.
This week at Hacky Hour UQ, Anne who is creating an R module for single cell sequence analysis for 10’s of thousands of cells.
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.
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.
Co-founders of Hacky Hour
At Hacky Hour this week, the co-founders of Hacky Hour UQ, Sam Hames (left, in red) and Belinda Weaver (right, in white).
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.
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