Workshops
Variant Calling with Galaxy and the GVL for beginners
In this tutorial we cover the concepts of detecting small variants (SNVs and indels) in human genomic DNA using a small set of reads from chromosome 22. The tutorial is designed to introduce the tools, datatypes and workflow of variant detection. We will align reads to the genome, look for differences between reads and reference genome sequence, and filter the detected genomic variation manually to understand the computational basis of variant calling.
Workshops
Introduction to Molecular Modelling & Visualisation for Life Sciences
This Melbourne Bioinformatics workshop introduces beginners to molecular modelling and visualisation techniques using packages such as VMD and NAMD. After introductory talks participants will be given practical exercises to visualise molecules as well as learn how to submit jobs to the Melbourne Bioinformatics clusters.
Workshops
Open source science with Git and GitHub
Learn how to keep a record your code’s evolution over time using the git version control system, used by companies and open-source projects worldwide. Git allows you to easily maintain snapshots of your code as you make changes, keep multiple parallel versions of your code, and collaborate with others.
Workshops
Express your interest in a GATK Best Practice bioinformatics workshop
Bioplatforms Australia are calling for expressions of interest in a GATK Best Practice bioinformatics workshops.
The Genome Analysis Toolkit or GATK is a widely used software package developed by the Data Science and Data Engineering group at the Broad Institute, to perform variant discovery analysis on high-throughput sequencing data. This workshop will cover key concepts involved in applying the GATK Best Practices for variant discovery.
Please note: by submitting details you have NOT enrolled in a Bioplatforms Australia workshop and that the workshop modules that you have selected may not run. Due to limited resources they will only run a workshop once there is enough interest.
Workshops
Introduction to Galaxy and the GVL
Galaxy is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research. It allows users without programming experience to easily specify parameters and run individual tools as well as larger workflows. It also captures run information so that any user can repeat and understand a complete computational analysis. Finally, it allows users to share and publish analyses via the web.
This beginners workshop will introduce Galaxy’s interface, tool use, histories, and workflows and get new users of the Genomics Virtual Laboratory up and running.
This is a hands-on workshop and attendees should bring their own laptops.
Workshops
RNA-Seq Differential Gene Expression Analysis using Galaxy and the GVL
In this tutorial we will cover the concepts of RNA-Seq differential gene expression (DGE) analysis using Galaxy: an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.
Participants with no previous Galaxy experience are strongly recommended to attend the “Introduction to Galaxy” workshop first.
Attendees are required to bring their own laptop computers.
Workshops
Intermediate Molecular Modelling & Visualisation for Life Sciences
This workshop is for the intermediate user who is already familiar with molecular modelling and submitting cluster jobs, and is interested in learning more advanced job submission and visualisation techniques.
Topics include: advanced job submission scripts; data analysis; and molecular image and movie making.
Participants are required to bring their own laptop computers with VMD or PyMol installed.
Workshops
Introduction to Unix
Knowledge of the Unix operating system is fundamental to being productive on HPC systems such as those offered by Melbourne Bioinformatics. This workshop will introduce you to the fundamental Unix concepts by way of a series of hands-on exercises.
Workshops
Introduction to High Performance Computing
Using High Performance Computing (HPC) resources such as Melbourne Bioinformatics in an effective and efficient manner is key to modern research. This workshop will introduce you to HPC environments and assist you to get on with your research.
Other
ANDS health & medical research data, lunchtime webinar #1
WEBINAR 1: Funders and Publishers: What is being asked of researchers?
The Australian National Data Service (ANDS) invite you to join our series of three short 30 minute lunchtime webinars which aim to support better management and publication of Health and Medical data. ANDS is an NCRIS facility whose core purpose is to make Australia’s research data assets more valuable for researchers, research institutions and the nation.
These webinars are free and all ANDS materials are licensed Creative Commons CC-BY to enable easy reuse and re-purposing.
Who would benefit from attending?
- Researchers
- Medical Research Institutes
- Universities
- Clinician researchers at hospitals
- Research students (honours, Masters, PhD)
- Medical librarians and data managers who deal with sensitive data
Speaker list and full webinar details
The webinars will address commonly held concerns from within the health and medical research field around data publication.
Contact Kate LeMay for more information.
These webinars will be recorded. If you can’t attend please register and we will send you the recording and handout links.
Kate LeMay
Senior Research Data Specialist | Australian National Data Service
T: +61 2 6125 8538 | E: kate.lemay@nullands.org.au | W: ands.org.au
Twitter: @katelemayands ORCiD: orcid.org/0000-0002-2405-7365
Talk
A general overview of the Common Workflow Language and its use in bioinformatics
The Common Workflow Language (CWL) is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. CWL is developed by an informal, multi-vendor working group consisting of organisations and individuals aiming to enable scientists to share data analysis workflows.
Michael R. Crusoe is a Community Engineer and co-founder of the CWL Project and will present a seminar: A general overview of the Common Workflow Language and its use in bioinformatics.
When: 12:00-1:00pm Thu 11 May 2017 (no registration required)
Where: FW Jones Theatre, Level 3, Medical Building, University of Melbourne
Michael’s activities in Melbourne have been organised by Melbourne Bioinformatics, with sponsorship from the Computational Biology Research Initiative at the University of Melbourne.
This one-hour talk and a subsequent two-hour workshop Michael’s gave in Melbourne were recorded and are now accessible via our Video archive.
Other
ANDS health & medical research data, lunchtime webinar #2
WEBINAR 2: Storing and Publishing Health and Medical Data: Where can I store my data during and after my research project?
The Australian National Data Service (ANDS) invite you to join our series of three short 30 minute lunchtime webinars which aim to support better management and publication of Health and Medical data. ANDS is an NCRIS facility whose core purpose is to make Australia’s research data assets more valuable for researchers, research institutions and the nation.
These webinars are free and all ANDS materials are licensed Creative Commons CC-BY to enable easy reuse and re-purposing.
Who would benefit from attending?
- Researchers
- Medical Research Institutes
- Universities
- Clinician researchers at hospitals
- Research students (honours, Masters, PhD)
- Medical librarians and data managers who deal with sensitive data
Speaker list and full webinar details
The webinars will address commonly held concerns from within the health and medical research field around data publication.
Contact Kate LeMay for more information.
These webinars will be recorded. If you can’t attend please register and we will send you the recording and handout links.
Kate LeMay
Senior Research Data Specialist | Australian National Data Service
T: +61 2 6125 8538 | E: kate.lemay@nullands.org.au | W: ands.org.au
Twitter: @katelemayands ORCiD: orcid.org/0000-0002-2405-7365
Talk
Open source science with Git and GitHub
Learn how to keep a record your code’s evolution over time using the git version control system, used by companies and open-source projects worldwide. Git allows you to easily maintain snapshots of your code as you make changes, keep multiple parallel versions of your code, and collaborate with others.
Follow up with an understanding of GitHub, the king of open-source project hosting. Learn how you can use git and GitHub to do code review and contribute to your favourite open source projects.
This is a hands-on workshop. Attendees are required to bring their own laptop computers to participate.
Attendees should have some familiarity with the command line and a programming language of their choice.
Other
ANDS health & medical research data webinar series #3
WEBINAR 3: Ethics, Legal issues and data sharing: How can I obtain informed consent for sharing my data? What do I need to consider around storage, access, de-identification and plans for sharing? What laws impact upon the collection, handling and sharing of health and medical research data?
The Australian National Data Service (ANDS) invite you to join our series of three short 30-minute lunchtime webinars which aim to support better management and publication of Health and Medical data. ANDS is an NCRIS facility whose core purpose is to make Australia’s research data assets more valuable for researchers, research institutions and the nation.
These webinars are free and all ANDS materials are licensed Creative Commons CC-BY to enable easy reuse and re-purposing.
Who would benefit from attending?
- Researchers
- Medical Research Institutes
- Universities
- Clinician researchers at hospitals
- Research students (honours, Masters, PhD)
- Medical librarians and data managers who deal with sensitive data
Speaker list and full webinar details
The webinars will address commonly held concerns from within the health and medical research field around data publication.
Contact Kate LeMay for more information.
These webinars will be recorded. If you can’t attend please register and we will send you the recording and handout links.
Kate LeMay
Senior Research Data Specialist | Australian National Data Service
T: +61 2 6125 8538 | E: kate.lemay@nullands.org.au | W: ands.org.au
Twitter: @katelemayands ORCiD: orcid.org/0000-0002-2405-7365
Conference
VIZBI 2017, the 8th International Meeting on Visualising Biological Data
This conference will run from 14–16 June 2017.
VIZBI highlights best of breed computational data visualisation tools in many different fields of biology, and features 21 high profile speakers. Since VIZBI 2017 will be held in Australia for the first time, we believe it could be of interest to many within your life science department, especially those relying on computational tools for data visualisation and analysis.
VIZBI 2017 features keynotes from Daniel Keim, Tamara Munzner, and Drew Berry, in addition to talks from 18 world-leading researchers showcasing visualisations transforming how life scientists view data, and driving key advances in molecular biology, systems biology, biomedical science, and ecology.
The conference brings together a diverse community, including bioinformaticians, data scientists, computer scientists, and experimentalists, as well as medical illustrators, graphic designers, and graphic artists. VIZBI 2017 will also be part of Vivid Sydney – a spectacular festival of light, music, and ideas – strong synergies between these events give extra incentive to make the trip to Sydney.
