Software Carpentry with Python

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Software Carpentry's mission is to help researchers get more done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

• Hosted by: Centre for eResearch
• Date: July 11-12th
• Time: 8:30 - 16:30 rm 303-B05

More info and register

Software Carpentry with R

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Software Carpentry's mission is to help researchers get more done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

• Hosted by: Bioinformatics Institute and NZGL
• Date: July 11-12th
• Time: 8:30 - 16:30 rm 303-B07

More info and register

Research Data Management

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Why? Research funders and journal publishers increasingly require researchers to make their research data available for discovery and reuse. University guidance states that research data be stored for a minimum of 6 years. Effective management of your research data reduces loss, saves time, facilitates collaboration and increases the impact of your research.

The University of Auckland is developing Research Data Management (RDM) services to meet these increasing requirements, a collaboration between Libraries and Learning Services and the Centre for eResearch.

Who? Aimed at all staff researchers and PhD candidates interested in storing, sharing and publishing their research data and increasing the impact of their research.

What? Workshop provides an introduction to research data management concepts and the support and services at the University of Auckland, including demonstration of the University's Data Publishing and Discovery Service - auckland.figshare.com Attendees will develop strategies for capturing and organising research data, explore options around publishing, sharing and reusing data, and start to draft a Data Management Plan.

• Hosted by: Centre for eResearch and Libraries and Learning Services
• Date: July 13th
• Time: 10:00 - 12:00 rm 303-B05

Register

Genome Assembly, Annotation and Visualisation

Understanding and using genomic data is of critical importance. In this one-day workshop, you will:

• Assemble a small genome de novo, and understand the process of assembly and quality assessment of genomes.
• Generate annotations by predicting genes and genomic features in a genome, and understand the theory and limitations of gene prediction.
• Understand genome annotations, and visualise and interpret your annotations in a genome browser.
• Discuss new technologies (e.g long-read and single-molecule sequencing, single-cell genomics) and their uses and limitations.

• Hosted by: Bioinformatics Institute and NZGL
• Date: July 13th
• Time: 9:00 - 17:00 rm 303-B07

Register your expression of interest in this workshop

Research Virtual Machines

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Do your computations take too long on your laptop? Do you want to offload long-running simulations to a different computer? Are there computations you cannot run on your desktop because you don't have enough memory or compute power? Find out about the University of Auckland's Research Virtual Machine Service. We'll talk about what a research virtual machine is, how you work with a virtual machine, how a virtual machine can help you with your research, and how to request one.

• Hosted by: Centre for eResearch
• Date: July 13th
• Time: 14:00 - 14:45 rm 303-B05

No need to register - just come along!

Increase Your Impact

You’ve published your research, now what?

Join us for an overview of how the library can help you get your research more widely read and how you can measure that impact. Facilitators: Rosanne van Leeuwen, Emma Richardson, Vanessa Bruell

• Hosted by: Libraries and Learning Services
• Date: July 13th
• Time: 13:00 - 14:00 rm 303-B11

Register

Know Your (Copy)Rights

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What you need to know about copyright before you publish your work – find out how to maintain rights over your work. After a brief presentation, Melanie will be available to answer individual questions. Facilitator: Melanie Johnson, Copyright Officer

• Hosted by: Libraries and Learning Services
• Date: July 13th
• Time: 14:00 - 14:45 rm 303-B11

Register

Transcriptomics

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Transcriptomics (using Next-Generation Sequencing) is a fast-moving area which continues to see developments in data analysis, experimental design, and sequencing technologies. In this one-day workshop, you will:

• Design and analyse an RNA-seq experiment (both with and without a reference genome) using current versions of the Tuxedo and Trinity workflows.
• Use ERCC spike-in controls and the ercc dashboard to define the lower limit of detection, dynamic range of your experiment, and to detect any biases introduced during the experiment.
• Visualise your results, both at the whole-transcriptome level and at the level of the individual gene.
• Discuss emerging sequencing technologies (e.g. molecular indexing, single-cell transcriptomics, long-read technologies) that can add significant value to your experimental design, and the state of bioinformatic tools used to exploit these technologies.

• Hosted by: Bioinformatics Institute and NZGL
• Date: July 14th
• Time: 9:00 - 17:00 rm 303-B07

Register your expression of interest in this workshop

Genomics Analysis with Geneious

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Learn the basics of genomic analysis in Geneious.

This workshop will cover handling NGS data, de novo assembly, map to reference, SNP calling, and annotating genomes. There will also be an open Q&A session at the end where you can ask any other questions you have about Geneious.

• Hosted by: Biomatters
• Date: July 14th
• Time: 9:00 - 12:00 rm 303-B11

Register

Introduction to HPC

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The New Zealand eScience Infrastructure (NeSI) provides New Zealand researchers, including those based at the University of Auckland, with access to High Performance Computing (HPC). In this session we will discuss what we mean when we say HPC, how to assess if HPC may be able to help your research, and - if HPC is for you - how to get access to it.

• Hosted by: NeSI
• Date: July 14th
• Time: 10:00 - 11:00 rm 303-B05

No need to register - just come along!

HPC Ask an expert

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Have you always wondered whether or not your research could benefit from taking the leap to HPC? Come and talk to one of the experts… No question is a dumb question!

• Hosted by: NeSI
• Date: July 14th
• Time: 13:00 - 15:00 rm 303-B05

No need to register - just come along!

HackyHour

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Hacky Hour is a shared space and place where students and researchers can congregate to work on their research problems related to code, data, or digital tools in a social environment.

Inspired by #ResBaz and initiatives at Melbourne Uni we are building a community @ UoA to share skills and knowledge across disciplinary boundaries. Hacky Hour is an open and inclusive environment, all are welcome to join in. With support from the Centre for eResearch there are knowledgeable folk around who can help you with your research or technical questions.

Join us from 3-4pm @ Strata Cafe every Thursday

• Hosted by: Centre for eResearch
• Date: July 14th
• Time: 15:00 - 16:00 Strata Cafe

No need to register - just come along!

Library Drop-in Sessions

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• Want to know more about and sign-up for ORCiD, researcher ID?
• Have issues around sharing /storing research data?
• Keen to publish data?
• Learn about our UoA Data Publishing and Discovery Service - auckland.figshare.com
• Find out how Subject Librarians can help you - literature searching and the use of Library resources, acquiring resources, referencing, workshops and individual consultations, and liaison to so much more.
• Interested in increasing your impact and using social media to communicate your research?

Research Support Services and Subject Librarians will be available to answer these and more queries; no booking required.

• Hosted by: Libraries and Learning Services
• Dates and Times: July 11th - 12:00 to 13:00 and July 14th - 13:00-15:00
• Where: 303-B11

No need to register - just come along!

Metabarcoding

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Metabarcoding allows for rapid analysis of the species diversity present in populations. In this one-day workshop, you will:

• Understand the use of positive and negative controls and mock communities.
• Demultiplex samples using fastq_multx (if samples contain more than one amplicon).
• Ensure that reads are properly paired using SolexaQA++ lengthsort.
• Generate OTU tables and assign taxonomy using VSEARCH and QIIME.
• Use QIIME to calculate diversity within and between samples and visualise the results.

• Hosted by: Bioinformatics Institute and NZGL
• Date: July 15th
• Time: 9:00 - 17:00 rm 303-B07

Register your expression of interest in this workshop

Introduction to OpenMP

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Know the value of parallelising your code but not sure where to start, or maybe you're not even sure how parallelisation could help your research? OpenMP provides an API for parallelising your research on your desk-top. In this workshop we will discuss how this could help your research and start to take you through how to approach using OpenMP. Bring along your laptop and be prepared to optimise your research!

• Hosted by: NeSI
• Date: July 15th
• Time: 09:30 - 10:30 rm 303-B05

Register

Introduction to MPI

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Now that you understand the value of parallelising your code, this session will discuss how this approach can be applied to distributed-memory machines (i.e. taking your parallel code from your desktop to an HPC system).

• Hosted by: NeSI
• Date: July 15th
• Time: 11:00 - 12:00 rm 303-B05

Register

Computational phylogenetics using BEAST 2

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Bayesian computational methods have transformed the study of evolutionary processes, yielding deep quantitative insights into the ancestral histories of genes, populations and species. This workshop will be composed of two parts, the first of which will bring participants up to speed on the statistical theory behind these methods. The second part will be a tutorial during which participants will learn to infer phylogenetic trees and ancestral population dynamics from real genetic data using the BEAST 2 software package

• Hosted by: Centre for Computational Evolution
• Date: July 15th
• Time: 13:00 - 16:00 rm 303-B11

Register