Upcoming Events

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.

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.

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.

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.

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.

Prerequisite: Plotting & Programming in Python, or Python competence gained otherwise.

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.

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.

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.

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

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

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

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

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"

Group Meeting:  "Embracing genetic diversity: GBRS pipline"

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

A demo of CellProfiler for image analysis.

A one-hour science reading and writing workshop.

Presenter: Lunn Sawyer

Location: ERB 1419

Time: 1:30pm

Location: ERB 1419

Presenter: Petr Simecek

Location: ERB 1419

ERB 1419

ERB 1419

ERB 1419

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