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What's ITN up to?
What's ITN up to?
Visit this page to find out about recent ITN events, software updates, publications, new projects, and more!
Workshops at University of Michigan
Workshops at University of Michigan
ITN recently gave a series of workshops at the University of Michigan in Ann Arbor. We partnered with Kim Zuhlke and Erik Roys.
ITN recently gave a series of workshops at the University of Michigan in Ann Arbor. We partnered with Kim Zuhlke and Erik Roys.
The 2 day workshop series featured many informatics topics including:
The 2 day workshop series featured many informatics topics including:
Reproducibility Practices for Informatics
Version Control with GitHub
Containers with Docker
Usage of AI to help with transparency
Clinical Data Analysis
Single Cell and Bulk RNAseq
Spatial Transcriptomics
Resources available at the University of Michigan
The workshops also featured ITCR sponsored tools including GenePattern and spatialGE, as well as others including PositCloud and various R packages. We collaborated with speakers and Chris Battiston, Ted Liefeld, Oscar Ospina, and Olivia Koues to deliver these workshops.
The workshops also featured ITCR sponsored tools including GenePattern and spatialGE, as well as others including PositCloud and various R packages. We collaborated with speakers and Chris Battiston, Ted Liefeld, Oscar Ospina, and Olivia Koues to deliver these workshops.
The ITN team had a great time getting to know informatics researchers at the University of Michigan, Wayne State, and other nearby institutions.
The ITN team had a great time getting to know informatics researchers at the University of Michigan, Wayne State, and other nearby institutions.
In the first reproducibility workshop, Candace Savonen talked about a variety of practices and tools to perform more transparent research. We also walked through how to use GitHub to track changes in files over time.
In the first reproducibility workshop, Candace Savonen talked about a variety of practices and tools to perform more transparent research. We also walked through how to use GitHub to track changes in files over time.
In our next reproducibility workshop, Candace Savonen talked about the use of containers such as Docker to help collaborators have consistent computing environments. We also discussed how GitHub actions can be used to test analyses with different computing environments.
In our next reproducibility workshop, Candace Savonen talked about the use of containers such as Docker to help collaborators have consistent computing environments. We also discussed how GitHub actions can be used to test analyses with different computing environments.
In the clinical data workshop, led by Chris Battiston we discussed general topics related to data management and analysis. We also discussed Kaplan-Meier curves and R packages to analyze clinical data over time.
In the clinical data workshop, led by Chris Battiston we discussed general topics related to data management and analysis. We also discussed Kaplan-Meier curves and R packages to analyze clinical data over time.
sqlr - data management
ggplot2 - visualizations
survival - analyzing survival data
survminer - publication ready survival analysis data plots
In day 2 of our workshop series we started the day with a discussion led by Kate Isaac about bulk RNA sequencing and single cell RNA sequencing.
In day 2 of our workshop series we started the day with a discussion led by Kate Isaac about bulk RNA sequencing and single cell RNA sequencing.
Oscar Ospina joined us to deliver a workshop about spatial transcriptomics. He discussed many of the tools available as well as important considerations for study design.
Oscar Ospina joined us to deliver a workshop about spatial transcriptomics. He discussed many of the tools available as well as important considerations for study design.
Olivia Koues gave an overview of the methods and services available at the University of Michigan Core.
Olivia Koues gave an overview of the methods and services available at the University of Michigan Core.
Introducing OTTRProJect!
Introducing OTTRProJect!
Our Open-source Tools for Training Resources (OTTR) software repositories are now all together on https://github.com/ottrproject!
Our Open-source Tools for Training Resources (OTTR) software repositories are now all together on https://github.com/ottrproject!
New Cheatsheets!
New Cheatsheets!
New cheatsheets available for using our software OTTR and for scientific engagement and networking. Check them out on our new page: https://www.itcrtraining.org/resources/cheatsheets
New cheatsheets available for using our software OTTR and for scientific engagement and networking. Check them out on our new page: https://www.itcrtraining.org/resources/cheatsheets
We made our cheatsheets in an automated modular way, as we often have similar documentation steps across multiple processes. Check out our code on GitHub. It could be helpful for making your own software documentation! More development to make this easier for others to use coming soon!
We made our cheatsheets in an automated modular way, as we often have similar documentation steps across multiple processes. Check out our code on GitHub. It could be helpful for making your own software documentation! More development to make this easier for others to use coming soon!
Workshop Series at Moffitt Cancer Center
Workshop Series at Moffitt Cancer Center
We recently partnered with Jeremy Goecks, Maria Isaza, Brooke Fridley, Xiaoqing Yu, and speakers Oscar Ospina, Xiaofei (Sophia) Song, Alex Soupir, and Paulo Cilas Morais Lyra Junior at the Moffitt Cancer Center in Tampa, Florida. The 2 day workshop series featured many informatics topics including:
We recently partnered with Jeremy Goecks, Maria Isaza, Brooke Fridley, Xiaoqing Yu, and speakers Oscar Ospina, Xiaofei (Sophia) Song, Alex Soupir, and Paulo Cilas Morais Lyra Junior at the Moffitt Cancer Center in Tampa, Florida. The 2 day workshop series featured many informatics topics including:
Computing resources for cancer research
Data Ethics
Single Cell RNA Sequencing
Spatial Transcriptomics
Single Cell Protein Imaging
Machine Learning to predict treatment outcomes
The workshops also featured ITCR sponsored tools including Galaxy and spatialGE, as well as others including spatialTIME, PositCloud, Seurat, and PyCaret.
The workshops also featured ITCR sponsored tools including Galaxy and spatialGE, as well as others including spatialTIME, PositCloud, Seurat, and PyCaret.
In our first workshop, Carrie Wright talked about the fundamentals of how computing resources work, as well as important data ethics considerations for cancer research.
Kate Isaac then got the workshop attendees started on Galaxy.
In our second workshop, Xiaofei (Sophia) Song guided us through an overview of single cell RNA sequencing.
Kate Isaac then guided learners through a single cell RNA seq activity on Galaxy.
In our third workshop, Oscar Ospina guided us through an overview of spatial transcriptomics.
Oscar then helped the learners work through a spatial transcriptomics activity using spatialGE.
The next day, Alex Soupir, Candace Savonen, and Julia Wroble helped learners get familiar with single cell protein imaging data and analysis.
This included using data from the VectraPolarisData Package.
Elizabeth Humphries then walked through a single cell protein imaging activity using spatialTIME on PositCloud.
In our final workshop, Paulo Cilas Morais Lyra Junior, helped learners reproduce a Machine Learning study that predicted cancer patient outcomes with immune checkpoint blockade therapy.
This included a machine learning activity using PyCaret on Galaxy led by Kate Isaac.
ITN Podcast Gets a Shout-out
ITN Podcast Gets a Shout-out
Our podcast, Cracking the Cancer Code, was recently featured in the news for the Center for Biomedical Informatics & Information Technology by the National Cancer Institute (NCI). You can listen to our podcast at: https://crackingthecancercode.buzzsprout.com/.
Our podcast, Cracking the Cancer Code, was recently featured in the news for the Center for Biomedical Informatics & Information Technology by the National Cancer Institute (NCI). You can listen to our podcast at: https://crackingthecancercode.buzzsprout.com/.
Workshops at The ITCR 2024 Annual Meeting
Workshops at The ITCR 2024 Annual Meeting
We delivered three workshops at the annual meeting in Indianapolis, including workshops on:
We delivered three workshops at the annual meeting in Indianapolis, including workshops on:
1) Practices for reproducibility using GitHub and GitHub Actions
1) Practices for reproducibility using GitHub and GitHub Actions
2) Using containers like Docker for research
2) Using containers like Docker for research
A big thanks to Oscar Ospina and Brooke Fridley who partnered with us in delivering the spatial transcriptomics workshop!
A big thanks to Oscar Ospina and Brooke Fridley who partnered with us in delivering the spatial transcriptomics workshop!
Workshop Series at NIH
Workshop Series at NIH
We recently partnered with the QIIME2 team, lead by Dr. Greg Caporaso at the Pathogen and Microbiome Institute, Northern Arizona University to deliver a series of workshops at the National Institutes of Health (NIH). QIIME2 is a widely used and highly cited microbiome data science platform and ITCR-funded. The 3 day workshop series featured many hands-on activities using QIIME2, as well as other content related to containers, computing, reproducibility, and more.
We recently partnered with the QIIME2 team, lead by Dr. Greg Caporaso at the Pathogen and Microbiome Institute, Northern Arizona University to deliver a series of workshops at the National Institutes of Health (NIH). QIIME2 is a widely used and highly cited microbiome data science platform and ITCR-funded. The 3 day workshop series featured many hands-on activities using QIIME2, as well as other content related to containers, computing, reproducibility, and more.
The QIIMME 2 team included: Chloe Herman, Hannah Hagen, and Colin Wood, as well as guest QIIME2 developer, Colin Brislawn.
Candace Savonen talked about concepts in reproducibility and led a workshop about the command line, as well as Docker and Podman for scientists.
Kate Isaac showed us how to get started using tools like QIIME2 on Galaxy.
Carrie Wright talked about cloud computing and ITN resources.
Greg Caporaso gave an overview of the QIIME2 workflow and resources.
Hannah Hagen led workshop activities about microbiome metadata and provenance in QIIME2.
Chloe Herman led workshop activites about microbiome diversity and engraftment analysis.
Workshop Series at NYU
Workshop Series at NYU
We recently partnered with Dr. Drew Jones at the New York University and delivered a series of workshops on a variety of cancer informatics topics including gene expression analysis, computing for cancer Informatics, and AI for research.
We recently partnered with Dr. Drew Jones at the New York University and delivered a series of workshops on a variety of cancer informatics topics including gene expression analysis, computing for cancer Informatics, and AI for research.
Candace Savonen talked about how to use the ITCR funded tool GenePattern for gene expression analysis. Ted Liefeld helped partner with us from GenePattern for the activity.
Kate Isaac talked about the fundamentals of gene expression data, including different types of biases, as well as how to use the ITCR funded tool Galaxy for bioinformatics research.
Carrie Wright talked about fundamentals of computer hardware and cloud computing, as well as AI ethics.
Candace Savonen also talked about how Large Language Models (LLMs) work today.
New Publication in Bioinformatics!
New Publication in Bioinformatics!
In collaboration with the ITCR OPEN group, we published a paper about practices that support software designed for biomedical research and how we might consider the impact of such tools. This includes some research evaluating how various practices (such as tweeting about a tool, having in-depth documentation, or showcasing badges about build status) might associate with the frequency with which papers mention software. Check out our paper published by Bioinformatics: https://doi.org/10.1093/bioinformatics/btae469
In collaboration with the ITCR OPEN group, we published a paper about practices that support software designed for biomedical research and how we might consider the impact of such tools. This includes some research evaluating how various practices (such as tweeting about a tool, having in-depth documentation, or showcasing badges about build status) might associate with the frequency with which papers mention software. Check out our paper published by Bioinformatics: https://doi.org/10.1093/bioinformatics/btae469
ITN Workshops at Hutch were a Success!
ITN Workshops at Hutch were a Success!
Attendees came from Fred Hutchinson Cancer Center, Seattle Children's Hospital, and the University of Washington.
Attendees came from Fred Hutchinson Cancer Center, Seattle Children's Hospital, and the University of Washington.
Ava Hoffman presented a workshop about creating Data Management and Sharing Plans for NIH proposals.
Ava Hoffman presented a workshop about creating Data Management and Sharing Plans for NIH proposals.
Ava Hoffman, Carrie Wright, and Elizabeth Humphries (with content from Candace Savonen) presented a workshop about AI Considerations for Research.
Ava Hoffman, Carrie Wright, and Elizabeth Humphries (with content from Candace Savonen) presented a workshop about AI Considerations for Research.
Carrie Wright presented a workshop about using LaTeX and Overleaf to create scientific article preprints.
Carrie Wright presented a workshop about using LaTeX and Overleaf to create scientific article preprints.
ITN Package gets a shoutout!
ITN Package gets a shoutout!
Our package Metricminer, which helps scientist track the usage of their software and outreach efforts, was featured in an article for https://datascience.cancer.gov/!
Our package Metricminer, which helps scientist track the usage of their software and outreach efforts, was featured in an article for https://datascience.cancer.gov/!
Train the TRAINER Citizen Science event - SEATTLE, WA
Train the TRAINER Citizen Science event - SEATTLE, WA
May 3, 2024, from 11 AM -3 PM
This workshop is a collaborative initiative between community organizers, advocates, researchers, and practitioners dedicated to addressing cancer disparities. The workshop focuses on the integrated use of Citizen scientists and Cancer Informatics as a model of engagement in cancer research and practice. The initial lineup of featured presenters for the Train-the-Trainer Spring 2024 workshop includes professional leaders and researchers from Fred Hutchinson, Morehouse School of Medicine and the University of Illinois at Chicago.
May 3, 2024, from 11 AM -3 PM
This workshop is a collaborative initiative between community organizers, advocates, researchers, and practitioners dedicated to addressing cancer disparities. The workshop focuses on the integrated use of Citizen scientists and Cancer Informatics as a model of engagement in cancer research and practice. The initial lineup of featured presenters for the Train-the-Trainer Spring 2024 workshop includes professional leaders and researchers from Fred Hutchinson, Morehouse School of Medicine and the University of Illinois at Chicago.
Photo by John Cameron on Unsplash
ITN is now on LinkedIN
ITN is now on LinkedIN
We now have a profile on LinkedIn! Follow us here: https://www.linkedin.com/company/101136872/
New Software on Cran!
New Software on Cran!
We created a new R package that is now on CRAN to help people more easily collect metrics from various places. Check it out here: https://hutchdatascience.org/metricminer/
Course on LatEX and Overleaf on Coursera
Course on LatEX and Overleaf on Coursera
Our course introducing learners to writing smarter with Overleaf and LaTeX is now available on Coursera.
New Courses on AI!
New Courses on AI!
We have created 4 minicourses that are part of a larger course on AI for Decision Makers. You can take the courses on Coursera if you already have a membership or access the materials here. We will launch the courses on Leanpub soon!
Take the mini courses on Coursera:
New Cancer Data Science Challenge Website!
New Cancer Data Science Challenge Website!
Our colleagues at Sage Bionetworks have created a new website called OpenChallenges.io, which helps connect people to biomedical challenges to accelerate citizen science and data benchmarking.
Check out the current challenges!
Loqui Supports Subtitles
Loqui Supports Subtitles
Loqui, an interactive web application that helps you create videos from slides (Microsoft PowerPoint or Google Slides), now supports subtitles! You can download a text file in .srt format, complete with timestamped subtitles, or embed these subtitles directly into your videos. This lets you easily upload subtitled videos to Youtube by uploading your mp4 video file and including subtitles by uploading the srt file generated by Loqui.
You can try Loqui out here: https://loqui.fredhutch.org/
ITN education content gets a shout out!
ITN education content gets a shout out!
The National Cancer Institute Center for Biomedical Informatics and Information Technology has created a new cancer data science resource that includes some of the ITN's materials and more.
Check out the wide variety of cancer data science training resources on datascience.cancer.gov! Whether you are new to the field or a seasoned researcher looking to expand your data science skills, you’ll find basic resources, free courses, tips, and more in the new section!
our Poster at AACR Conference in Orlando RECEIVED special designation
our Poster at AACR Conference in Orlando RECEIVED special designation
Our team, including Maisha Standifer (a partner at the Morehouse school of medicine), Le’Chaun Kendall, and Rohan Jeremiah presented a poster titled Increasing cancer-related community-engagement strategies among Historically Black Colleges and Universities and Minority Serving Institutions (A047) at the AACR science of cancer health disparities in racial/ethnic minorities and the medically underserved conference. The conference selection committee gave our poster a special Patient Advocate Designation. See here for a relevant paper.
AACR_23_UE5_FINAL_POSTER 2023 09 29[12].pdf
ITN Workshops at the Annual ITCR meeting covered reproducibility practices
ITN Workshops at the Annual ITCR meeting covered reproducibility practices
Candace Savonen led two workshops at the ITCR 2023 annual meeting. The first introduced trainees to the pull request process using Git and GitHub for version control and code review. The second introduced concepts related to automation using GitHub Actions.
LOQui Now supports Google Slides and PowerPoint
LOQui Now supports Google Slides and PowerPoint
Loqui which is a web-based app that helps you create videos from slides (both from Power Point or Google Slides). The notes become the audio, and the slides become the images. You can try Loqui out here: https://loqui.fredhutch.org/
ITN Events at the Fred Hutchinson Cancer Center Were a Hit!
ITN Events at the Fred Hutchinson Cancer Center Were a Hit!
ITN delivered 4 workshops in August 2023 at the Fred Hutchinson Cancer Center in Seattle, Washington, engaging with numerous cancer researchers, post docs, students, and scientists, covering a variety of topics.
A Genomics Tools Workshop featured the UCSC Xena Browser
A Genomics Tools Workshop featured the UCSC Xena Browser
Candace Savonen provided general guidance for genomics research and directed attendees to ITN resources for learning about what to do with various types of genomic data (including content about whole genome sequencing from Claire Mills).
Cailin Jordan (a Hutch graduate student) gave a presentation about sc-ATAC-Seq
Jacob Greene (a Hutch graduate student) gave a presentation about ChIP-Seq
Mary Goldman gave a demonstration of how the UCSC Xena Browser can help visualize many aspects of genomics research. The Xena Browser is an online exploration tool for public and private, multi-omic and clinical/phenotype data.
A Cancer Computing Workshop helped attendees learn more about resources
A Cancer Computing Workshop helped attendees learn more about resources
Carrie Wright taught about how computers work, the evolution of computing, how shared and cloud computing resources work, and resources for cancer research computing, including Galaxy and the Hutch computing cluster (available to Hutch employees).
An AI Workshop helped Attendees learn how to harness the power of AI for their daily work
An AI Workshop helped Attendees learn how to harness the power of AI for their daily work
Candace Savonen and Elizabeth Humphries taught about how to craft useful prompts, how to work with chatbots ethically, and the differences between many of the current popular Chatbots and tools.
A Workshop about multidisciplinary teams and DEI help attendees learn practices for effectively working in teams
A Workshop about multidisciplinary teams and DEI help attendees learn practices for effectively working in teams
Carrie Wright taught about best practices for finding, creating, and nurturing multidisciplinary teams, as well as for helping to support team members with diverse scientific backgrounds and life experiences.
ITN Events at TGEN were interactive!
ITN Events at TGEN were interactive!
ITN delivered 2 workshops in August 2023 at Translational Genomics Research Institute (TGEN) in Phoenix, Arizona.
Attendees from the Native American Cancer Prevention (NACP) Partnership, TGEN and the University of Arizona, and Northern Arizona University joined us to learn about cancer computing resources, like Galaxy and microbiome analysis.
Greg Caporaso gave a demonstration of QIIME2, a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.
ITN reached out at the NCI junior Investigator meeting
ITN reached out at the NCI junior Investigator meeting
Howard Baek presented about ITN courses, software, and more at the 2023 annual National Cancer Institute (NCI) Junior Investigator meeting with a poster, short talk, and lunch session.
ITN Got a shout out on the Cancer Data Science Pulse Blog
ITN Got a shout out on the Cancer Data Science Pulse Blog
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology blog called the Cancer Data Science Pulse featured the ITN in a post February 1, 2022 titled NCI’s ITCR Training Network Puts Cancer Research Tools and Training at Your Fingertips.
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