Upcoming Events

Containerization with Singularity
Friday, October 23, 2020

Do you use software containers? Have you heard of applications such as Docker and Singularity, but aren't sure where to begin with incorporating them into your workflows? Join us for an introductory workshop hosted by the Research IT Cyberinfrastructure Team. In this four-hour workshop, you will learn: 

  • What a container is
  • Why Singularity is our containerization platform of choice
  • How to build containers from scratch and interact with them
  • How to use Docker containers with Singularity
  • How to leverage Singularity to optimize your current scientific workflows

Singularity represents an exciting new frontier in HPC application development moving on to our newly built research cluster. Come join us and learn how Singularity can help you make your workflows more reproducible and mobile. 

Who: The course is aimed at graduate students and other researchers at the Jackson Laboratory. For IT security reasons, external participants will not be admitted. You don't need to have any previous knowledge of the tools that will be presented at the workshop. 

Find more information on the workshop website.

 

Data Carpentry
Tuesday, October 13, 2020

Tuesdays and Thursdays, Oct 13-22

 

Data Carpentry aims to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. This workshop uses a tabular ecology dataset and teaches data cleaning, management, analysis and visualization. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. 

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop. 

Find more information and registration on the workshop website.

Introduction to High Performance Computing
Tuesday, September 29, 2020

Online

This workshop introduces high performance computing using the Jackson Laboratory’s computing cluster. The goal is to teach novice programmers to use powerful tools and computing resources, and to engage in best practices for using these resources. The emphasis of this workshop is to give attendees a strong foundation in the fundamentals of the bash shell and to teach best practices for scientific computing in high performance computing environments. By the end of this workshop, participants will be able to: 

·         Use the UNIX command line to operate a computer, connect to a cluster, and write simple shell scripts. 

·         Submit and manage jobs on a cluster using a scheduler, transfer files, and use software through environment modules. 

Prerequisites: If you have stored files on a computer at all and recognize the word “file” and either “directory” or “folder” (two common words for the same thing), you’re ready for this workshop.  

Who: This course is intended for Jackson Laboratory researchers only. For IT security reasons, external participants will not be admitted.  

Find more information on the workshop website.

Statistics Study Group
Wednesday, September 2, 2020

Every other Wednesday in 2020

Find more information on the statistics study group schedule.

Introduction to Image Analysis with Fiji
Thursday, March 12, 2020

Introduction to Image Analysis with Fiji

Thu-Fri, Mar 12-13

Holt Conference Room, JGM & Bioinformatics Training Room, JMG

Register

 

Automated microscopy technologies have amplified the volume and complexity of image data such that  biologists must rely on computer scientists for solutions and software. Fiji provides a huge variety of advanced image analysis solutions and a friendly user interface for researchers to develop innovative, cutting-edge pipelines for biological image analysis. Users range from non-programmers to bioinformaticians and software engineers to professional computer science researchers. Biologists without programming skills can use Fiji to search for biologically relevant features (segmentation), to follow relevant objects across space and time (tracking) and to compare specimens through mapping to anatomical or cellular digital atlases. Those skilled in programming can use scripting languages in Fiji to build custom image-processing pipelines. Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji is Just ImageJ. 

In this workshop, we will introduce basic concepts of image analysis and intermediate workflows using Fiji. By the end of this workshop, you will be able to automate the bulk your image analysis, making it faster, more consistent and reproducible. 

Prerequisites: None. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Susan McClatchy
Statistical Inference for Biology
Tuesday, March 10, 2020

Statistical Inference for Biology

Tuesdays, Mar 10-24, 9am to 12:30pm

Bioinformatics Training Room, JMG

Register

Statistical Inference for Biology will introduce the statistical concepts essential to understanding p-values and confidence intervals. Lecture and demonstration in concepts will precede guided hands-on practice and coaching for skills development so that participants can perform statistical analysis with good understanding. At the end of the series, participants will be able to:

  • define a population, sample, estimate, and parameter
  • describe null and normal distributions
  • explain why confidence intervals, not p-values, better reflect statistical significance
  • calculate power
  • perform permutation and association tests

The course will follow Irizarry & Love’s Data Analysis for the Life Sciences and is aimed at graduate students and other researchers who would like to learn more about statistics.

Prerequisite: Competence with the R programming language. 

Find more information on the workshop website.

Susan McClatchy
Introduction to High Performance Computing
Friday, March 6, 2020

Introduction to High Performance Computing

Fri, Mar 6

Holt Conference Room, JGM & Bioinformatics Training Room, JMG

Register

This workshop introduces high performance computing using the Jackson Laboratory’s computing cluster. The goal is to teach novice programmers to use powerful tools and computing resources, and to engage in best practices for using these resources. The emphasis of this workshop is to give attendees a strong foundation in the fundamentals of the bash shell and to teach best practices for scientific computing in high performance computing environments. The course is aimed at graduate students and other researchers. 

Prerequisites: None. You don't need to have any previous knowledge of the tools that will be presented at the workshop. By the end of this workshop, participants will be able to:

 

  • Use the UNIX command line to operate a computer, connect to a cluster, and write simple shell scripts.
  • Submit and manage jobs on a cluster using a scheduler, transfer files, and use software through environment modules.
  • Find, create, and manage Singularity containers.

Find more information on the workshop website.

Susan McClatchy
Software Carpentry
Thursday, February 27, 2020

Software Carpentry

Thu-Fri, Feb 27-28

Holt Conference Room, JGM

Register

 

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. The course is aimed at graduate students and other researchers.

Prerequisites: None. You don't need to have any previous knowledge of the tools that will be presented at the workshop. Participants will learn to:

  • Automate Tasks with the Unix Shell
  • Build Programs with Python
  • Version Control with Git

This is a good way to learn Python, which is a prerequisite for our more advanced courses in image processing and machine learning. Python emphasizes code readability and productivity, and is excellent for engineering analysis pipelines.

You can find more information on the workshop website.

Susan McClatchy
Data Carpentry Genomics
Thursday, January 30, 2020

Data Carpentry Genomics, Jan 30-31, Farmington

A two-day workshop from 9am-4:30pm

This workshop teaches data management and analysis for genomics research including: best practices for organization of bioinformatics projects and data, use of command line utilities, use of command line tools to analyze sequence quality and perform variant calling, and connecting to and using cloud computing. The training assumes no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts, including the concept of genomic variation within a population. By the end of the workshop, learners will be able to:

    1. Structure their metadata, organize and document their genomics data and bioinformatics workflow, and access data on the NCBI sequence read archive (SRA) database,

    2. Navigate their file systems, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards,

    3. Use command-line tools to perform quality control, align reads to a reference genome, and identify and visualize between-sample variation,

    4. Work with Amazon AWS cloud computing and transfer data between their local computer and cloud resources.

Participants must attend in person at the Jackson Laboratory for Genomic Medicine in Farmington, CT.  Remote attendance from desks, home, or away will not be supported.

Please complete the Registration form to participate.

More information is available on the workshop website.

Susan McClatchy
Statistics with R Study Group
Tuesday, January 14, 2020

Statistics with R Study Group, Tuesdays, 11am-12pm

A one-hour weekly study group from Jan 14-Mar 3

Statistics with R Study Group will explore Irizarry & Love’s Data Analysis for the Life Sciences. This book starts with one of the most critical areas in statistics and in the life sciences: statistical inference. Other topics include exploratory data analysis, matrix algebra, statistical models, and distance and dimension reduction. Study group sessions feature problem-solving and challenges in a cooperative setting. Rather than have an instructor lead us through the book, we’ll study chapters on our own and meet for one hour to solve the exercises together. This study group is aimed those who would like to learn more about statistics for high-throughput data. Study group participants can meet other group members in person at the Jackson Laboratory campuses in Bar Harbor or Farmington or can attend remotely via WebEx.  

Prerequisite: Basic competence with the R programming language. 

Please complete the Registration form to participate.

You can find more information on the study group website.

Susan McClatchy
Python Study Group
Wednesday, December 4, 2019

Dec 4, 6, 11, 13, 18, 20 from 11am to 12pm

We’ll launch an intermediate Python study group to explore the Pandas (short for panel data) library. Pandas aims to close the gap in the richness of data analysis tools in Python and the numerous domain-specific statistical computing platforms and database languages. We'll study chapter 4 of Jake VanderPlas' Python Data Science Handbook on our own time, then challenge each other with exercises during twice-weekly one-hour meetings. For more information and registration, please visit the workshop website. Study group meetings will be held via WebEx, though participants can meet other group members in person in Bar Harbor and Farmington.

PrerequisitePlotting & Programming in Python, or Python competence gained otherwise.

Susan McClatchy
The Unix Shell
Saturday, November 9, 2019

DECEMBER 9th & 16th; 1-4pm: We’ll offer a beginner Unix shell series starting Mon Dec 9 in both Farmington and Bar Harbor. The course will meet Monday afternoons for 2 sessions ending Dec 16. Use of the shell is fundamental to using a wide range of other powerful tools and computing resources (including “high-performance computing” supercomputers and cloud computing resources). These lessons will start you on a path towards using these resources effectively. For more information and registration, please visit the workshop website.

Susan McClatchy
Shiny
Friday, October 25, 2019

To be held in Bar Harbor and Farmington JAX campuses.

This intermediate level course introduces Shiny for interactive data visualization. Shiny is an R package that makes it easy to build interactive web apps straight from R so that you and others can interact with your data and your analysis. This workshop provides a fresh, interactive approach to telling your data story. For more information and registration, visit the workshop website.

We hope to see you at one of these R workshops this month.

Susan MClatchy
R for Data Science
Thursday, October 17, 2019

This beginner course provides essential data wrangling skills including data organization, formatting, and cleaning, and will be held in both Bar Harbor and Farmington JAX campuses.

Later sessions progress to data visualization and more from the free book R for Data Science by Garrett Grolemund and Hadley Wickham of RStudio. There will be time at the end of each session for participants to practice newfound skills on their own data. No programming experience is expected or required.

For more information and registration, visit the workshop website.

Suan McClatchy
Plotting and Programming in Python
Wednesday, October 16, 2019

Oct 16, 23, and 30 in Bar Harbor and Farmington

This weekly Wednesday afternoon series is an introduction to programming in Python for people with little or no previous programming experience. It uses plotting as its motivating example.

Image Analysis Hackathon
Thursday, October 10, 2019

The goal of this monthly hackathon is to share skills, collaborate on projects, and build community around image analysis.

Susan McClatchy
Girls Who Code
Wednesday, September 25, 2019

Starting Wed Sep 25 and continuing every Wed that school is in session at the Jesup Memorial Library in Bar Harbor, Maine. Girls Who Code is on a mission to close the gender gap in technology and to change the image of what a programmer looks like and does.

Susan McClatchy
R for Reproducible Scientific Analysis
Wednesday, August 28, 2019

A 2-day workshop in programming with R at the University of Maine Orono. EVENT INFO

Susan McClatchy
Quantitative Trait Mapping
Thursday, August 22, 2019

A 2 day workshop in genetic mapping for the Diversity Outbred in Bar Harbor, ME. EVENT INFO

Susan McClatchy
Carpentry Instructor Training
Monday, July 29, 2019

A two-day workshop in best practices for teaching computing and data analysis in Farmington, CT. EVENT INFO

Susan McClatchy
Image Analysis with scikit-image
Wednesday, July 17, 2019

A two-day workshop in image analysis, July 17-18 in Bar Harbor, ME. EVENT INFO

Susan McClatchy
Quantitative Trait Mapping
Thursday, June 13, 2019

A 2 day workshop in the qtl2 package for R at the University of North Carolina. EVENT INFO

Susan McClatchy
Introduction to High Performance Computing
Monday, June 10, 2019

A one-day workshop for JAX employees only in Bar Harbor, ME. EVENT INFO

Susan McClatchy
17th Annual Meeting of the Complex Trait Community
Sunday, June 9, 2019

The Churchill Lab will be attending the 17th Annual Meeting of the Complex Trait Community, in collaboration with the Rat Genomics Community. The meeting will be held in La Jolla, California on the University of California San Diego campus from Sunday, June 9 to Tuesday, June 11, 2019.

 

Presenters from the Churchill Lab will be:

 

  • Gary Churchill: "The Genetic Architecture of Insulin Secretion"
     
  • Greg Keele: "Integrative QTL analysis of gene expression and chromatin accessiblility identifies multi-tissue patterns of genetic regulation"
     
  • Isabela Gyuricza: "Differential gene and protein expression from the aging heart of Diversit Oubred mice"
     
  • Andrew Deighan: "Hematologic Predictors of Lifespan in Diversity Outbred Mice"
     
  • Duy Pham: "Genetic Drivers of Protein Expression in Pancreatic Islet Cells"

 

 

Introduction to High Performance Computing
Friday, June 7, 2019

A one-day workshop for JAX employees only in Farmington, CT. EVENT INFO

Susan McClatchy
R for Reproducible Scientific Analysis
Thursday, June 6, 2019

A 2-day workshop in programming with R in Bar Harbor, ME. EVENT INFO

Susan McClatchy
Guest Seminar
Tuesday, May 14, 2019

Adam Freund, Ph.D., Principal Investigator at Calico will presenting a seminar on May 14th at the Jackson Laboratory.
Title: "A network approach to studying aging"

Adam Freund, Ph.D.
R for Reproducible Scientific Analysis
Monday, May 13, 2019

A 2-day workshop in programming with R at Bates College. EVENT INFO

Susan McClatchy
KB Choi
Wednesday, May 8, 2019

Group Meeting:  "Embracing genetic diversity: GBRS pipline"

KB Choi
Group Meeting
Wednesday, May 1, 2019

KB Choi will present "Embracing genetic diversity: GBRS pipeline"

KB Choi
R for Data Science
Wednesday, May 1, 2019

A Wednesday morning intermediate series for data science with R in Farmington, CT. EVENT INFO

Susan McClatchy
R for Reproducible Scientific Analysis
Tuesday, April 2, 2019

A 2-day workshop in programming with R in Farmington, CT. EVENT INFO

Susan McClatchy
Basic Image Analysis with Python
Thursday, March 28, 2019

A 1.5-day workshop in image analysis, Mar 28-29 in Bar Harbor, ME. EVENT INFO

Susan McClatchy
Plotting & Programming in Python
Wednesday, March 27, 2019

A 1.5-day workshop in Python, Mar 27-28 in Bar Harbor, ME. EVENT INFO

Susan McClatchy
Data Carpentry Ecology
Monday, March 25, 2019

A two-day workshop in data cleaning, management, analysis and visualization at Bigelow Laboratory, Boothbay Harbor, ME. EVENT INFO

Susan McClatchy
Introduction to High Performance Computing
Wednesday, March 20, 2019

A one-day workshop for JAX employees only in Farmington, CT. EVENT INFO

Susan McClatchy
R for Data Science
Monday, February 25, 2019

A Monday afternoon intermediate series for data science with R in Bar Harbor, ME. EVENT INFO

Susan McClatchy
Basic Image Analysis with Python
Thursday, January 31, 2019

A 1.5-day workshop in image analysis, Jan 31 & Feb 1 in Farmington, CT. EVENT INFO

Susan McClatchy
Basic Image Analysis with Python
Thursday, January 31, 2019

A 1.5-day workshop in image analysis, Jan 31 & Feb 1 in Farmington, CT. EVENT INFO

Susan McClatchy
Plotting & Programming in Python
Wednesday, January 30, 2019

A 1.5-day workshop in Python, Jan 30-31 in Farmington, CT. EVENT INFO

Susan McClatchy
R for Reproducible Scientific Analysis
Monday, January 28, 2019

A Monday afternoon beginner series for programming with R in Bar Harbor, ME. EVENT INFO

Susan McClatchy
Introduction to High Performance Computing
Friday, December 7, 2018

A one-day workshop for JAX employees only in Farmington, CT. EVENT INFO

Susan McClatchy
Data Carpentry Genomics
Tuesday, November 6, 2018

A two-day workshop in  data management and analysis for genomics research in Farmington, CT. EVENT INFO

Susan McClatchy
Introduction to High Performance Computing
Monday, October 22, 2018

A one-day workshop for JAX employees only in Bar Harbor, ME. EVENT INFO

Susan McClatchy
Bioconductor Workshop
Wednesday, October 17, 2018

A one-day workshop in Bioconductor in Farmington, CT. EVENT INFO

Susan McClatchy
R for Reproducible Scientific Analysis
Monday, October 15, 2018

A 2-day workshop in programming with R in Farmington, CT. EVENT INFO

Susan McClatchy
Bioconductor Workshop
Friday, October 12, 2018

A one-day workshop in Bioconductor in Bar Harbor, ME. EVENT INFO

Susan McClatchy
R for Reproducible Scientific Analysis
Wednesday, October 10, 2018

A two-day workshop in programming with R, held in Bar Harbor, ME. EVENT INFO

Susan McClatchy
Bioconductor Train-the-Trainers
Thursday, September 27, 2018

A one-day workshop in teaching Bioconductor in Bar Harbor, ME. EVENT INFO

Susan McClatchy
Data Carpentry Ecology
Monday, September 10, 2018

A two-day workshop in data cleaning, management, analysis and visualization

Susan McClatchy
Carpentry Instructor Training
Tuesday, August 28, 2018

A two-day workshop in best practices for teaching computing and data analysis, held in Farmington, CT. EVENT INFO

Susan McClatchy
Carpentries Instructor Training
Wednesday, August 8, 2018

A two-day workshop in best practices for teaching computing and data analysis, online. EVENT INFO

Susan McClatchy
Software Carpentry
Tuesday, July 24, 2018

A two-day workshop in the Unix shell, Python, and git in Farmington, CT. EVENT INFO

Susan McClatchy
Plotting and Programming with Python
Thursday, June 14, 2018

A two-day workshop in plotting and programming with Python in Bar Harbor, ME. EVENT INFO

Susan McClatchy
Carpentry Instructor Training
Monday, June 11, 2018

A two-day workshop in best practices for teaching computing and data analysis in Bar Harbor, ME. EVENT INFO

Susan McClatchy
R for Reproducible Scientific Analysis
Thursday, June 7, 2018

A two-day workshop in programming with R in Bar Harbor, ME. EVENT INFO

Susan McClatchy
R for Reproducible Scientific Analysis
Monday, April 2, 2018

A 1.5-day workshop in programming with R in Farmington, CT. EVENT INFO

Susan McClatchy
Quantitative Trait Mapping
Tuesday, March 20, 2018

A 1.5 day workshop in the qtl2 package for R in Bar Harbor, ME. EVENT INFO

Susan McClatchy
R for Reproducible Scientific Analysis
Wednesday, March 14, 2018

A two-day workshop in programming with R in Bar Harbor, ME. EVENT INFO

Susan McClatchy
Programming with Python
Tuesday, February 6, 2018

A two-day workshop in programming with Python in Bar Harbor, Maine. EVENT INFO

Susan McClatchy
Quantitative Trait Mapping
Thursday, January 18, 2018

A one-day workshop in the qtl2 package for R in Bar Harbor, ME. EVENT INFO

Susan McClatchy
R for Reproducible Scientific Analysis
Tuesday, January 16, 2018

A two-day workshop in programming with R in Bar Harbor, Maine. 9am-4:30pm. EVENT INFO

Susan McClatchy
R for Reproducible Scientific Analysis
Tuesday, January 9, 2018

A two-day workshop in programming with R at Tufts-Sackler Graduate School of Biomedical Sciences. 9am to 4:30pm. EVENT LINK

Dog Genetics Lectures
Friday, September 15, 2017

In collaboration with the Jesup Library, Daniel Gatti in the Churchill lab will be speaking about dog genetics and will present the results of ancestry analysis on dogs that live on MDI.

Jesup_JAX_Dog_Flyer.pdf

Daniel Gatti
Software Carpentry R
Wednesday, June 14, 2017

A two-day workshop in best practices for reproducible research with R.

High Performance Computing
Thursday, June 8, 2017
Dog DNA Sample Collection
Saturday, May 20, 2017

Join us at the Jesup Library from 12 noon to 4 PM with your dog for dog DNA sample collection. We will be collecting DNA via a cheek swab and will send the sample to Neogen where your dog will be genotyped at over 170,000 SNPs. The cost is $105 per dog and all of the money goes to Geneseek. Dr. Gatti will be performing the data analysis free of charge and will present the results in mid-September.

Daniel Gatti, Ph.D.
Dog Genetics Lecture
Thursday, May 18, 2017

Join us for an evening lecture about dogs and dog genentic. Dr. Gatti will discuss recent advances in dog genetics and will explain how the ancestry of dogs can be inferred by DNA sequence data.  He will also explain the project that he is working on and what to expect when your dog is genotyped.

Daniel Gatti, Ph.D.
Image Analysis Group
Tuesday, May 16, 2017
Writers Group
Wednesday, May 3, 2017
Writers Group
Wednesday, April 26, 2017
Group meeting
Wednesday, February 8, 2017

Kidney and Heart pQTLs

Petr Simecek
Group Lab Meeting
Wednesday, November 2, 2016

Presenter: Lunn Sawyer

Location: ERB 1419

Time: 1:30pm

Group Lab Meeting
Wednesday, October 26, 2016

Presenter: Steve Munger

Location: ERB 1419

Time: 1:30pm

No Group Lab Meeting
Wednesday, October 19, 2016
Group Lab Meeting
Wednesday, October 12, 2016

Presenter: Steve Munger

Location: ERB 1419

Time: 1:30pm

No Group Lab Meeting
Wednesday, September 28, 2016
Group Lab Meeting
Wednesday, September 21, 2016

Location: ERB 1419

Presenter: Narayanan Raghupathy

Group Lab Meeting
Wednesday, September 14, 2016

Location: ERB 1419

Presenter: Petr Simecek

Group Lab Meeting
Wednesday, September 7, 2016

Location: ERB 1419

Presenter: Gary Churchill

Group Lab Meeting
Wednesday, August 31, 2016

Location: ERB 1419

Presenter: KB Choi
Group Meeting
Wednesday, August 3, 2016

ERB 1419

Maddy Williams & Elliot Krause (Churchill Lab Summer Students)
Group Meeting
Wednesday, July 27, 2016

ERB 1419

Xingyao Chen & Clifton Jeffery (Churchill Lab Co-Op Students)
Group Meeting
Wednesday, July 20, 2016

ERB 1419

Brian Geuther (Kumar Lab)
Group Meeting
Wednesday, July 13, 2016

ERB 1419

NO MEETING
Group Meeting
Wednesday, July 6, 2016

ERB 1419

NO MEETING
Group Meeting
Wednesday, June 29, 2016

ERB 1419

Steve Munger
Group Meeting
Wednesday, June 22, 2016

TBA

Gary Churchill
Data Carpentry Genomics Workshop
Thursday, April 14, 2016

The focus of this workshop will be on working with genomics data and data management and analysis for genomics research.
B18 Staff Conference Room
link

Gary Churchill
Wednesday, June 17, 2015

Group Meeting

Gary Churchill
Dan Gatti
Wednesday, June 10, 2015

Group Meeting

Dan Gatti