CBC and CGI Workshop Registration
ISG CBC Workshop Schedule - 2023
Workshop: Virtual Single Cell RNA-seq
Dates: March 20-23, 2023 (4days)
Time: 9.00am - 1.00pm
Location: Virtual
Cost: $350 (UConn affiliates including UConn Health)
$483 (External Participants)
Registration Open link
Virtual Single Cell RNA-seq Workshop :: (Click here to expand)
Workshop schedule
Day 1: Introduction to Linux and high performance computing.
Day 2-4:
Understanding the Considerations while designing single-cell RNA-seq experiment
Hands on steps to convert raw single-cell RNA-seq data to a count or expression matrix
Compute and assess QC of the datasets
Clustering of Cells (UMAP, tSNE) and identify cluster specific markers and annotating cell types.
Perform integration of different sample conditions.
Perform trajectory analysis in cell differentiation.
Registration
Workshop FAQ
Who should attend?
Anyone with keen interest in Single Cell RNA-seq. Prior course participants have included faculty, post docs, grad students, advanced undergraduates, staff, and industry researchers.
What are the prerequisites?
Prior bioinformatic experience is not required. We have dedicated the first day of workshop to the basics of Linux and high performance computing.
What do I need?
You will need your own laptop to use, have a recent version of R, RStudio installed, and some other applications. We will send you details of softwares and installation instructions with your registration acknowledgement email.
Can I bring my own data?
We will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.
How much does it cost?
The registration fee is $483 and $350 for UConn affiliates. It is payable at the time of registration with credit card or KFS.
Where is the workshop?
It will be held virtually over Zoom, and will run from 9:00am to 12:00pm on the date indicated.
How do I apply?
All registration is “first-come, first-served.” There is no application process. Sign up as soon as possible to ensure your place in the workshop.
Questions?
If you have any questions, please don’t hesitate to contact us at cbcsupport@uconn.edu
Workshop: Virtual RAD-seq
Dates: April 17-20, 2023(4days)
Time: 9.00am - 12.00pm
Location: Online
Cost: $350 (UConn affiliates including UConn Health)
$483 (External Participants)
Registration Open link
Virtual RAD-seq Workshop :: (Click here to expand)
Workshop schedule
Day 1: Introduction to Linux and high performance computing.
Day 2-4:
The workshop will cover basic concepts and walk through a complete analysis on a high performance computing cluster. The analysis will start with raw reads and go through some very basic analyses of population genetic structure. The core learning goal is to familiarize attendees with the steps necessary to analyze RAD-seq data, the tools available, common data formats, and possible pitfalls they may encounter. The short duration of the workshop means that nearly all the time will be given to explaining the rationale and mechanics of each stage of the analysis, and not to independent exercises.
Registration
Workshop FAQ
Who should attend?
Anyone with keen interest in RAD-seq. Prior course participants have included faculty, post docs, grad students, advanced undergraduates, staff, and industry researchers.
What are the prerequisites?
Prior bioinformatic experience is not required. We have dedicated the first day of workshop to the basics of Linux and high performance computing.
What do I need?
You will need your own laptop. WE RECOMMEND PARTICIPANTS TO HAVE 2 DISPLAY UNITS (MONITORS), THIS WILL HELP YOU TO FOLLOW THE INSTRUCTOR ON ONE AND WILL LET YOU CARRY OUT THE EXERCISE ON THE OTHER. We will send you details of softwares and installation instructions with your registration acknowledgement email.
Can I bring my own data?
We will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.
How much does it cost?
The registration fee is $483 and $350 for UConn affiliates. It is payable at the time of registration with credit card or KFS.
Where is the workshop?
It will be held on Blackboard-Collaborate platform, and will run from 9:00am to 12:00pm on the date indicated.
How do I apply?
All registration is “first-come, first-served.” There is no application process. Sign up as soon as possible to ensure your place in the workshop.
Questions?
If you have any questions, please don’t hesitate to contact us at cbcsupport@uconn.edu
Workshop: Virtual Genome Annotation
Dates: June 12-15, 2023 (4days)
Time: 9.00am - 12.00pm
Location: Online
Cost: $350 (UConn affiliates including UConn Health)
$483 (External Participants)
Registration Open link
Virtual Genome Annotation Workshop :: (Click here to expand)
Workshop schedule
Day 1: Introduction to Linux and high performance computing.
Day 2: Introduction to HTS, Genome Assembly Validation, File Format Basics, and Repeats;
Day 3: Alignments, RNA-Seq based annotation with BRAKER2, and Functional Annotation;
Day 4: MAKER annotation, long reads annotation with BRAKER2, and evaluation
Registration
Workshop FAQ
Who should attend?
Anyone with keen interest in genome annotation. Prior course participants have included faculty, post docs, grad students, advanced undergraduates, staff, and industry researchers.
What are the prerequisites?
Prior bioinformatic experience is not required. We have dedicated the first day of workshop to the basics of Linux and high performance computing.
What do I need?
You will need your own laptop to use, have a recent version of R, RStudio installed, and some other applications. We will send you details of softwares and installation instructions with your registration acknowledgement email.
Can I bring my own data?
We will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.
How much does it cost?
The registration fee is $483 and $350 for UConn affiliates. It is payable at the time of registration with credit card or KFS.
Where is the workshop?
It will be held on Blackboard-Collaborate platform, and will run from 9:00am to 12:00pm on the date indicated.
How do I apply?
All registration is “first-come, first-served.” There is no application process. Sign up as soon as possible to ensure your place in the workshop.
Questions?
If you have any questions, please don’t hesitate to contact us at cbcsupport@uconn.edu
Workshop: Virtual Genome Assembly
Dates: July 17-20, 2023 (4days)
Time: 9.00am - 12.00pm
Location: Online
Cost: $350 (UConn affiliates including UConn Health)
$483 (External Participants)
Registration Open link
Virtual Genome Assembly Workshop :: (Click here to expand)
Workshop schedule
Day 1: Introduction to Linux, HPC, HTS
Day 2-4 : Introduction to k-mer plots, high throughput sequencing, quality control of sequence data, contaminant detection, Genome assembly strategies and short-read assembly, Long-read and hybrid assembly, post-processing, assembly benchmarking
Registration
Workshop FAQ
Who should attend?
Anyone with keen interest in Genome Assembly methods. Prior course participants have included faculty, post docs, grad students, advanced undergraduates, staff, and industry researchers.
What are the prerequisites?
Prior bioinformatic experience is not required. We have dedicated the first day of workshop to the basics of Linux and high performance computing.
What do I need?
You will need your own laptop to use, have a recent version of R, RStudio installed, and some other applications. We will send you details of softwares and installation instructions with your registration acknowledgement email.
Can I bring my own data?
We will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.
How much does it cost?
The registration fee is $483 and $350 for UConn affiliates. It is payable at the time of registration with credit card or KFS.
Where is the workshop?
It will be held on Blackboard-Collaborate platform, and will run from 9:00am to 12:00pm on the date indicated.
How do I apply?
All registration is “first-come, first-served.” There is no application process. Sign up as soon as possible to ensure your place in the workshop.
Questions?
If you have any questions, please don’t hesitate to contact us at cbcsupport@uconn.edu
Past Workshops
Workshop: Virtual (Non-model) RNA-seq Data Analysis
Dates: February 13-16, 2023 (4 days)
Time: 9.00am - 12.00pm
Location: Online
Cost: $350 (UConn affiliates including UConn Health)
$483 (External Participants)
Registration Closed link
Virtual RNA-seq (Non-model) Workshop :: (Click here to expand)
Workshop schedule
Day 1: Introduction to Linux and high performance computing.
Day 2-4:
Introduction to Linux, high performance computing, high-throughput sequencing, and RNA-seq experimental design. Data Analysis: raw reads (fastq), read quality control, transcriptome assembly, filtering contigs and clustering, EnTAP annotation, Kallisto Indexing and feature quantification, introduction to R, DE analysis and visualization (DESeq2) GoAnalysis, Q&A.
Registration
Workshop FAQ
Who should attend?
Anyone with keen interest in transcriptomics and RNA-seq. Prior course participants have included faculty, post docs, grad students, advanced undergraduates, staff, and industry researchers.
What are the prerequisites?
Prior bioinformatic experience is not required. We have dedicated the first day of workshop to the basics of Linux and high performance computing.
What do I need?
You will need your own laptop. WE RECOMMEND PARTICIPANTS TO HAVE 2 DISPLAY UNITS (MONITORS), THIS WILL HELP YOU TO FOLLOW THE INSTRUCTOR ON ONE AND WILL LET YOU CARRY OUT THE EXERCISE ON THE OTHER. We will send you details of softwares and installation instructions with your registration acknowledgement email.
Can I bring my own data?
We will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.
How much does it cost?
The registration fee is $483 and $350 for UConn affiliates. It is payable at the time of registration with credit card or KFS.
Where is the workshop?
It will be held on Blackboard-Collaborate platform, and will run from 9:00am to 12:00pm on the date indicated.
How do I apply?
All registration is “first-come, first-served.” There is no application process. Sign up as soon as possible to ensure your place in the workshop.
Questions?
If you have any questions, please don’t hesitate to contact us at cbcsupport@uconn.edu
Workshop: Virtual RNA-seq (Model) Data Analysis
Dates: January 9-12, 2023 (4 days)
Time: 9.00am - 12.00pm
Location: Online
Cost: $350 (UConn affiliates including UConn Health)
$483 (External Participants)
Registration Closed link
Virtual RNA-seq Workshop :: (Click here to expand)
Workshop schedule
Day 1: Introduction to Linux and high performance computing.
Day 2-4:
This workshop will focus on experimental design, high throughput sequencing basics, quality control, alignment to a reference genome, differential expression analysis, and functional annotation. Tools presented are appropriate for researchers working in systems with a reference genome.
Registration
Workshop FAQ
Who should attend?
Anyone with keen interest in RNA-seq. Prior course participants have included faculty, post docs, grad students, advanced undergraduates, staff, and industry researchers.
What are the prerequisites?
Prior bioinformatic experience is not required. We have dedicated the first day of workshop to the basics of Linux and high performance computing.
What do I need?
You will need your own laptop. WE RECOMMEND PARTICIPANTS TO HAVE 2 DISPLAY UNITS (MONITORS), THIS WILL HELP YOU TO FOLLOW THE INSTRUCTOR ON ONE AND WILL LET YOU CARRY OUT THE EXERCISE ON THE OTHER. We will send you details of softwares and installation instructions with your registration acknowledgement email.
Can I bring my own data?
We will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.
How much does it cost?
The registration fee is $483 and $350 for UConn affiliates. It is payable at the time of registration with credit card or KFS.
Where is the workshop?
It will be held on Blackboard-Collaborate platform, and will run from 9:00am to 12:00pm on the date indicated.
How do I apply?
All registration is “first-come, first-served.” There is no application process. Sign up as soon as possible to ensure your place in the workshop.
Questions?
If you have any questions, please don’t hesitate to contact us at cbcsupport@uconn.edu
Workshop: Virtual Genome Assembly
Dates: May 16-19, 2022 (4days)
Time: 9.00am - 12.00pm
Location: Online
Cost: $350 (UConn affiliates including UConn Health)
$483 (External Participants)
Registration Closed link
Virtual Genome Assembly Workshop :: (Click here to expand)
Workshop schedule
Day 1: Introduction to Linux, HPC, HTS
Day 2-4 : Introduction to k-mer plots, high throughput sequencing, quality control of sequence data, contaminant detection, Genome assembly strategies and short-read assembly, Long-read and hybrid assembly, post-processing, assembly benchmarking
Registration
Workshop FAQ
Who should attend?
Anyone with keen interest in Genome Assembly methods. Prior course participants have included faculty, post docs, grad students, advanced undergraduates, staff, and industry researchers.
What are the prerequisites?
Prior bioinformatic experience is not required. We have dedicated the first day of workshop to the basics of Linux and high performance computing.
What do I need?
You will need your own laptop to use, have a recent version of R, RStudio installed, and some other applications. We will send you details of softwares and installation instructions with your registration acknowledgement email.
Can I bring my own data?
We will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.
How much does it cost?
The registration fee is $483 and $350 for UConn affiliates. It is payable at the time of registration with credit card or KFS.
Where is the workshop?
It will be held on Blackboard-Collaborate platform, and will run from 9:00am to 12:00pm on the date indicated.
How do I apply?
All registration is “first-come, first-served.” There is no application process. Sign up as soon as possible to ensure your place in the workshop.
Questions?
If you have any questions, please don’t hesitate to contact us at cbcsupport@uconn.edu
Workshop: Virtual RAD-seq
Dates: June 6-9, 2022(4days)
Time: 9.00am - 12.00pm
Location: Online
Cost: $350 (UConn affiliates including UConn Health)
$483 (External Participants)
Registration Closed link
Virtual RAD-seq Workshop :: (Click here to expand)
Workshop schedule
Day 1: Introduction to Linux and high performance computing.
Day 2-4:
The workshop will cover basic concepts and walk through a complete analysis on a high performance computing cluster. The analysis will start with raw reads and go through some very basic analyses of population genetic structure. The core learning goal is to familiarize attendees with the steps necessary to analyze RAD-seq data, the tools available, common data formats, and possible pitfalls they may encounter. The short duration of the workshop means that nearly all the time will be given to explaining the rationale and mechanics of each stage of the analysis, and not to independent exercises.
Registration
Workshop FAQ
Who should attend?
Anyone with keen interest in RAD-seq. Prior course participants have included faculty, post docs, grad students, advanced undergraduates, staff, and industry researchers.
What are the prerequisites?
Prior bioinformatic experience is not required. We have dedicated the first day of workshop to the basics of Linux and high performance computing.
What do I need?
You will need your own laptop. WE RECOMMEND PARTICIPANTS TO HAVE 2 DISPLAY UNITS (MONITORS), THIS WILL HELP YOU TO FOLLOW THE INSTRUCTOR ON ONE AND WILL LET YOU CARRY OUT THE EXERCISE ON THE OTHER. We will send you details of softwares and installation instructions with your registration acknowledgement email.
Can I bring my own data?
We will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.
How much does it cost?
The registration fee is $483 and $350 for UConn affiliates. It is payable at the time of registration with credit card or KFS.
Where is the workshop?
It will be held on Blackboard-Collaborate platform, and will run from 9:00am to 12:00pm on the date indicated.
How do I apply?
All registration is “first-come, first-served.” There is no application process. Sign up as soon as possible to ensure your place in the workshop.
Questions?
If you have any questions, please don’t hesitate to contact us at cbcsupport@uconn.edu
Workshop: Virtual Variant Detection
Dates: July 25-28, 2022 (4 days)
Time: 9.00am - 12.00pm
Location: Online
Cost: $350 (UConn affiliates including UConn Health)
$485 (External Participants)
Registration Closed link
Virtual Variant Detection Workshop :: (Click here to expand)
Workshop schedule
Day 1: Introduction to Linux, HPC, HTS, and experimental design for variant detection.
Day 2-4 :
Introduction, reference genome preparation, download and QC of sequence data, sequence alignment, QC and post-processing, variant detection using freebayes, GATK and bcftools, filtering and comparing variant sets, functional annotation, visualization.
Registration
Workshop FAQ
Who should attend?
Anyone with keen interest and desire to develop variant detection analytic skills. Prior course participants have included faculty, post docs, grad students, advanced undergraduates, staff, and industry researchers.
What are the prerequisites?
Prior bioinformatic experience is not required. We have dedicated the first day of workshop to the basics of Linux and high performance computing.
What do I need?
You will need your own laptop to use, have a recent version of R, RStudio installed, and some other applications. We will send you details of softwares and installation instructions with your registration acknowledgement email.
Can I bring my own data?
We will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.
How much does it cost?
The registration fee is $475 for external and $350 for UConn affiliates. It is payable at the time of registration with credit card or KFS.
Where is the workshop?
It will be held on Blackboard-Collaborate platform, and will run from 9:00am to 12:00pm on the date indicated.
How do I apply?
All registration is “first-come, first-served.” There is no application process. Sign up as soon as possible to ensure your place in the workshop.
Questions?
If you have any questions, please don’t hesitate to contact us at cbcsupport@uconn.edu
Workshop: Virtual HPC Introduction
Dates: October 24, 2022(1 day) This workshop has been postponed to Nov 14-17
Time: 8.30am - 12.00pm
Location: Online
Cost: $50
Registration Closed link
Virtual HPC Introduction Workshop :: (Click here to expand)
Workshop schedule
Day 1: Introduction to Linux and HPC
Registration
Registration Link
Workshop FAQ
Who should attend?
Anyone who is new to Linux programming and "High Performance Computing (HPC)" with keen interest in using Xanadu computational resources in their analysis. This workshop is aimed to train new and existing novice users. The workshop will start with hands on training of Linux and then the participants will be introduced with HPC concepts and will be trained to run interactive sessions, job submission (Batch and Array), job monitoring Running R and python sessions etc
What are the prerequisites?
Prior experience is not required.
What do I need?
You will need your own laptop to use.
How much does it cost?
The registration fee is $50. It is payable at the time of registration with credit card.
Where is the workshop?
It will be held on Blackboard-Collaborate platform, and will run from 9:00am to 12:00pm on the date indicated.
How do I apply?
All registration is "first-come, first-served." There is no application process. Sign up as soon as possible to ensure your place in the workshop.
Questions?
If you have any questions, please don’t hesitate to contact us at cbcsupport@uconn.edu
Workshop: Virtual Genome Annotation
Dates: October 24-27, 2022 (4days) This workshop has been postponed to Nov 14-17
Time: 9.00am - 12.00pm
Location: Online
Cost: $350 (UConn affiliates including UConn Health)
$483 (External Participants)
Registration Closed link
Virtual Genome Annotation Workshop :: (Click here to expand)
Workshop schedule
Day 1: Introduction to Linux and high performance computing.
Day 2: Introduction to HTS, Genome Assembly Validation, File Format Basics, and Repeats;
Day 3: Alignments, RNA-Seq based annotation with BRAKER2, and Functional Annotation;
Day 4: MAKER annotation, long reads annotation with BRAKER2, and evaluation
Registration
Registration Link
Workshop FAQ
Who should attend?
Anyone with keen interest in genome annotation. Prior course participants have included faculty, post docs, grad students, advanced undergraduates, staff, and industry researchers.
What are the prerequisites?
Prior bioinformatic experience is not required. We have dedicated the first day of workshop to the basics of Linux and high performance computing.
What do I need?
You will need your own laptop to use, have a recent version of R, RStudio installed, and some other applications. We will send you details of softwares and installation instructions with your registration acknowledgement email.
Can I bring my own data?
We will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.
How much does it cost?
The registration fee is $483 and $350 for UConn affiliates. It is payable at the time of registration with credit card or KFS.
Where is the workshop?
It will be held on Blackboard-Collaborate platform, and will run from 9:00am to 12:00pm on the date indicated.
How do I apply?
All registration is “first-come, first-served.” There is no application process. Sign up as soon as possible to ensure your place in the workshop.
Questions?
If you have any questions, please don’t hesitate to contact us at cbcsupport@uconn.edu
Workshop: Virtual HPC Introduction
Dates: November 14, 2022(1 day)
Time: 8.30am - 12.00pm
Location: Online
Cost: $50
Registration Closed link
Virtual HPC Introduction Workshop :: (Click here to expand)
Workshop schedule
Day 1: Introduction to Linux and HPC
Registration
Registration Link
Workshop FAQ
Who should attend?
Anyone who is new to Linux programming and "High Performance Computing (HPC)" with keen interest in using Xanadu computational resources in their analysis. This workshop is aimed to train new and existing novice users. The workshop will start with hands on training of Linux and then the participants will be introduced with HPC concepts and will be trained to run interactive sessions, job submission (Batch and Array), job monitoring Running R and python sessions etc
What are the prerequisites?
Prior experience is not required.
What do I need?
You will need your own laptop to use.
How much does it cost?
The registration fee is $50. It is payable at the time of registration with credit card.
Where is the workshop?
It will be held on Blackboard-Collaborate platform, and will run from 9:00am to 12:00pm on the date indicated.
How do I apply?
All registration is "first-come, first-served." There is no application process. Sign up as soon as possible to ensure your place in the workshop.
Questions?
If you have any questions, please don’t hesitate to contact us at cbcsupport@uconn.edu
Workshop: Virtual SingleCell RNASeq
Dates: November 14-17, 2022 (4days)
Time: 9.00am - 12.00pm
Location: Online
Cost: $350 (UConn affiliates including UConn Health)
$483 (External Participants)
Registration Closed link
Virtual SingleCell RNASeq Workshop :: (Click here to expand)
Workshop schedule
Day 1: Introduction to Linux and high performance computing.
Day 2:
Day 3:
Day 4:
Registration
Registration Link
Workshop FAQ
Who should attend?
Anyone with keen interest in genome annotation. Prior course participants have included faculty, post docs, grad students, advanced undergraduates, staff, and industry researchers.
What are the prerequisites?
Prior bioinformatic experience is not required. We have dedicated the first day of workshop to the basics of Linux and high performance computing.
What do I need?
You will need your own laptop to use, have a recent version of R, RStudio installed, and some other applications. We will send you details of softwares and installation instructions with your registration acknowledgement email.
Can I bring my own data?
We will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.
How much does it cost?
The registration fee is $483 and $350 for UConn affiliates. It is payable at the time of registration with credit card or KFS.
Where is the workshop?
It will be held on Blackboard-Collaborate platform, and will run from 9:00am to 12:00pm on the date indicated.
How do I apply?
All registration is “first-come, first-served.” There is no application process. Sign up as soon as possible to ensure your place in the workshop.
Questions?
If you have any questions, please don’t hesitate to contact us at cbcsupport@uconn.edu
Workshop: OpenRefine
Dates: December 13, 2022
Time: 9am- 11am
Location: Virtual
Cost: Free
Registration Closed link
OpenRefine : A visual data cleaning and exploration of messy data
TSV, CSV, *SV, Excel (.xls and .xlsx), JSON, XML, RDF as XML, and Google Data documents are all supported
“A power tool for working with messy data”
Explore - Get to know your data better
Clean - Standardise the data entries and fix any inconsistency with faceting, clustering, cell transforms, GREL expressions…
Enrich - Enrich your data by combining datasets from online resources/databases
Transform - easily subset, change the format, split/merge columns effortlessly, transpose columns/rows…
Automate - Annotate, record, and preserve your processing routine for transparency, then automate its reuse....
AWESOME FOR CLEANING CLINICAL TABULAR DATA !!!