Register training material
7 materials found

Keywords: Data visualisation  or Mass spectrometry 


WEBINAR: Making sense of phosphoproteomics data with Phosphomatics

This record includes training materials associated with the Australian BioCommons webinar  ‘Making sense of phosphoproteomics data with Phosphomatics’. This webinar took place on 2 June 2021.

Mass spectrometry-based phosphoproteomics is one of the most powerful tools available for investigating...

Keywords: Phosphoproteomics, Proteomics, Mass spectrometry

WEBINAR: Making sense of phosphoproteomics data with Phosphomatics https://dresa.org.au/materials/webinar-making-sense-of-phosphoproteomics-data-with-phosphomatics-a46784bd-7efe-4018-8893-761d1fcd32ba This record includes training materials associated with the Australian BioCommons webinar  ‘Making sense of phosphoproteomics data with Phosphomatics’. This webinar took place on 2 June 2021. Mass spectrometry-based phosphoproteomics is one of the most powerful tools available for investigating the detailed molecular events that occur in response to cellular stimuli. Experiments can routinely detect and quantify thousands of phosphorylated peptides, and interpreting this data, and extracting biological meaning, remains challenging.  This webinar provides an overview of the phosphoproteomics data analysis website, Phosphomatics, that incorporates a suite of tools and resources for statistical and functional analysis that aim to simplify the process of extracting meaningful insights from experimental results. Phosphomatics can natively import search and quantitation results from major search engines including MaxQuant and Proteome Discoverer and employs intuitive ‘wizards’ to guide users through data preprocessing routines such as filtering, normalization and transformation. A graphical platform of interactive univariate and multivariate analysis features is provided that allow subgroups of the uploaded data containing phosphosites of statistical interest to be created and interrogated through further functional analysis. A range of databases have been integrated that, for example, provide ligand and inhibitor information for key proteins or highlight key modification sites known to be involved in functional state regulation. At each step, published literature is natively incorporated along with a ‘bibliography builder’ that allows references of interest to be assembled and exported in various formats. Taken together, these expanded features aim to provide a ‘one-stop-shop’ for phosphoproteomics data analysis. The webinar is followed by a short Q&A session. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.   Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Phosphomatics -slides  (PDF and PPTX): Slides used in the presentation   Materials shared elsewhere: A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/_WpeL5t2DSI Melissa Burke (melissa@biocommons.org.au) Phosphoproteomics, Proteomics, Mass spectrometry
WEBINAR: Getting started with proteomics

This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with proteomics’. This webinar took place on 7 June 2023.

Event description 

Proteomics aims to identify and quantify all the proteins and peptides within a sample. Mass-spectrometry is...

Keywords: Bioinformatics, Proteomics, Mass spectrometry

WEBINAR: Getting started with proteomics https://dresa.org.au/materials/webinar-getting-started-with-proteomics-134c519c-0cea-4195-b444-1e73d551a20e This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with proteomics’. This webinar took place on 7 June 2023. Event description  Proteomics aims to identify and quantify all the proteins and peptides within a sample. Mass-spectrometry is the most common tool for proteomics and the wide array of methods, techniques and specialised approaches available have made it a popular method for probing cells, tissue and organisms in response to various stimuli or diseases. Each proteomics method has unique experimental design considerations and optimum workflows for data analysis meaning that there is no one-size-fits all solution. The variety of approaches available provides flexibility but can be bewildering and a barrier to getting started.  This webinar sets you up with the foundational knowledge of what to look out for when designing and understanding proteomics experiments. It outlines what you can and can’t do with proteomics, the type of data to expect as well as common data analysis approaches and quality control steps. This webinar was developed in collaboration with the Australian Core Facilities and Australian Proteomics Communities. Materials Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Getting started with proteomics_slides: A PDF copy of the slides presented during the webinar. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/RSrk2yqklQo Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Proteomics, Mass spectrometry
WORKSHOP: R: fundamental skills for biologists

This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.

 

Event description

Biologists need data analysis skills to be able to...

Keywords: Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation

WORKSHOP: R: fundamental skills for biologists https://dresa.org.au/materials/workshop-r-fundamental-skills-for-biologists-81aa00db-63ad-4962-a7ac-b885bf9f676b This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.   Event description Biologists need data analysis skills to be able to interpret, visualise and communicate their research results. While Excel can cover some data analysis needs, there is a better choice, particularly for large and complex datasets.  R is a free, open-source software and programming language that enables data exploration, statistical analysis, visualisation and more. The large variety of R packages available for analysing biological data make it a robust and flexible option for data of all shapes and sizes.  Getting started can be a little daunting for those without a background in statistics and programming. In this workshop we will equip you with the foundations for getting the most out of R and RStudio, an interactive way of structuring and keeping track of your work in R. Using biological data from a model of influenza infection, you will learn how to efficiently and reproducibly organise, read, wrangle, analyse, visualise and generate reports from your data in R. Topics covered in this workshop include: Spreadsheets, organising data and first steps with R Manipulating and analysing data with dplyr Data visualisation Summarized experiments and getting started with Bioconductor   This workshop is presented by the Australian BioCommons and Saskia Freytag from WEHI  with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Schedule (PDF): A breakdown of the topics and timings for the workshop Recommended resources (PDF): A list of resources recommended by trainers and participants Q_and_A(PDF): Archive of questions and their answers from the workshop Slack Channel. Materials shared elsewhere:   This workshop follows the tutorial ‘Introduction to data analysis with R and Bioconductor’ which is publicly available. https://saskiafreytag.github.io/biocommons-r-intro/ This is derived from material produced as part of The Carpentries Incubator project https://carpentries-incubator.github.io/bioc-intro/ Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
WEBINAR: Getting started with proteomics

This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with proteomics’. This webinar took place on 7 June 2023.

Event description 

Proteomics aims to identify and quantify all the proteins and peptides within a sample. Mass-spectrometry is...

Keywords: Bioinformatics, Proteomics, Mass spectrometry

WEBINAR: Getting started with proteomics https://dresa.org.au/materials/webinar-getting-started-with-proteomics This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with proteomics’. This webinar took place on 7 June 2023. Event description  Proteomics aims to identify and quantify all the proteins and peptides within a sample. Mass-spectrometry is the most common tool for proteomics and the wide array of methods, techniques and specialised approaches available have made it a popular method for probing cells, tissue and organisms in response to various stimuli or diseases. Each proteomics method has unique experimental design considerations and optimum workflows for data analysis meaning that there is no one-size-fits all solution. The variety of approaches available provides flexibility but can be bewildering and a barrier to getting started.  This webinar sets you up with the foundational knowledge of what to look out for when designing and understanding proteomics experiments. It outlines what you can and can’t do with proteomics, the type of data to expect as well as common data analysis approaches and quality control steps. This webinar was developed in collaboration with the Australian Core Facilities and Australian Proteomics Communities. Materials Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Getting started with proteomics_slides: A PDF copy of the slides presented during the webinar. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/RSrk2yqklQo Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Proteomics, Mass spectrometry
WORKSHOP: R: fundamental skills for biologists

This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.

Event description

Biologists need data analysis skills to be able to...

Keywords: Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation

WORKSHOP: R: fundamental skills for biologists https://dresa.org.au/materials/workshop-r-fundamental-skills-for-biologists This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022. **Event description** Biologists need data analysis skills to be able to interpret, visualise and communicate their research results. While Excel can cover some data analysis needs, there is a better choice, particularly for large and complex datasets.  R is a free, open-source software and programming language that enables data exploration, statistical analysis, visualisation and more. The large variety of R packages available for analysing biological data make it a robust and flexible option for data of all shapes and sizes.  Getting started can be a little daunting for those without a background in statistics and programming. In this workshop we will equip you with the foundations for getting the most out of R and RStudio, an interactive way of structuring and keeping track of your work in R. Using biological data from a model of influenza infection, you will learn how to efficiently and reproducibly organise, read, wrangle, analyse, visualise and generate reports from your data in R. Topics covered in this workshop include: - Spreadsheets, organising data and first steps with R - Manipulating and analysing data with dplyr - Data visualisation - Summarized experiments and getting started with Bioconductor This workshop is presented by the Australian BioCommons and Saskia Freytag from WEHI  with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. **Files and materials included in this record:** - Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. - Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. - Schedule (PDF): A breakdown of the topics and timings for the workshop - Recommended resources (PDF): A list of resources recommended by trainers and participants - Q_and_A(PDF): Archive of questions and their answers from the workshop Slack Channel. **Materials shared elsewhere:** This workshop follows the tutorial ‘Introduction to data analysis with R and Bioconductor’ which is publicly available. https://saskiafreytag.github.io/biocommons-r-intro/ This is derived from material produced as part of The Carpentries Incubator project https://carpentries-incubator.github.io/bioc-intro/ Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
Heurist Tutorials

A set of video tutorials with accompanying walkthroughs for building your first Heurist database and website. The first three tutorials show you how to get started in Heurist. The five subsequent tutorials introduce you to the five main menus in the Heurist interface.

Keywords: Heurist, Data management, Data visualisation, Digital Humanities, Databasing, website

Resource type: tutorial

Heurist Tutorials https://dresa.org.au/materials/heurist-tutorials A set of video tutorials with accompanying walkthroughs for building your first Heurist database and website. The first three tutorials show you how to get started in Heurist. The five subsequent tutorials introduce you to the five main menus in the Heurist interface. michael.falk@sydney.edu.au Johnson, Ian Osmakov, Artem Heurist, Data management, Data visualisation, Digital Humanities, Databasing, website mbr phd ecr researcher support
WEBINAR: Making sense of phosphoproteomics data with Phosphomatics

This record includes training materials associated with the Australian BioCommons webinar  ‘Making sense of phosphoproteomics data with Phosphomatics’. This webinar took place on 2 June 2021.

Mass spectrometry-based phosphoproteomics is one of the most powerful tools available for...

Keywords: Phosphoproteomics, Proteomics, Mass spectrometry

WEBINAR: Making sense of phosphoproteomics data with Phosphomatics https://dresa.org.au/materials/webinar-making-sense-of-phosphoproteomics-data-with-phosphomatics This record includes training materials associated with the Australian BioCommons webinar  ‘Making sense of phosphoproteomics data with Phosphomatics’. This webinar took place on 2 June 2021. Mass spectrometry-based phosphoproteomics is one of the most powerful tools available for investigating the detailed molecular events that occur in response to cellular stimuli. Experiments can routinely detect and quantify thousands of phosphorylated peptides, and interpreting this data, and extracting biological meaning, remains challenging.  This webinar provides an overview of the phosphoproteomics data analysis website, Phosphomatics, that incorporates a suite of tools and resources for statistical and functional analysis that aim to simplify the process of extracting meaningful insights from experimental results. Phosphomatics can natively import search and quantitation results from major search engines including MaxQuant and Proteome Discoverer and employs intuitive ‘wizards’ to guide users through data preprocessing routines such as filtering, normalization and transformation. A graphical platform of interactive univariate and multivariate analysis features is provided that allow subgroups of the uploaded data containing phosphosites of statistical interest to be created and interrogated through further functional analysis. A range of databases have been integrated that, for example, provide ligand and inhibitor information for key proteins or highlight key modification sites known to be involved in functional state regulation. At each step, published literature is natively incorporated along with a ‘bibliography builder’ that allows references of interest to be assembled and exported in various formats. Taken together, these expanded features aim to provide a ‘one-stop-shop’ for phosphoproteomics data analysis. The webinar is followed by a short Q&A session. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.   **Files and materials included in this record:** - Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. - Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. - Phosphomatics -slides  (PDF and PPTX): Slides used in the presentation **Materials shared elsewhere:** A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/_WpeL5t2DSI Melissa Burke (melissa@biocommons.org.au) Phosphoproteomics, Proteomics, Mass spectrometry