Fall Bioinformatics Seminars and Workshops

For more information, and to register, go to https://registration.genomecenter.ucdavis.edu/

 

So you want to do a Single Cell RNA-Seq Experiment

When:  Monday, November 6, 2017 1pm – 3pm

Where:  GBSF Auditorium

 

This FREE workshop is intended for those who are interested in and are in the planning stages of conducting a single-cell RNA-Seq experiment.  Topics to be discussed will include:

  • Experimental Design of scRNA-Seq experiments

  • Sample preparation, best practices

  • Single cell library prep and High throughput sequencing basics and choices

  • Cost estimation

  • Single Cell Analysis

    • Data cleanup and quality assurance

    • Mapping data

    • Assigning reads to cells and genes and counting

    • Analysis of single cell transcriptomics, tSNE plots, clustering, comparisons across samples

  • Downstream analysis/visualizations and tables

 

So you want to do an RNA-Seq Experiment/ Differential Gene Expression Analysis

When:  Tuesday, November 28, 2017 1pm – 3pm

Where:  GBSF Auditorium

 

This FREE workshop is intended for those who are interested in and are in the planning stages of conducting an RNA-Seq experiment.  Topics to be discussed will include:

  • Experimental Design of RNA-Seq experiment

  • Sample preparation, best practices

  • High throughput sequencing basics and choices

  • Cost estimation

  • Differential Gene Expression Analysis

    • Data cleanup and quality assurance

    • Mapping your data

    • Assigning reads to genes and counting

    • Analysis of differentially expressed genes

  • Downstream analysis/visualizations and tables

 

December 18-20:  Single Cell RNA-Seq Workshop

 

Presented topics will include experimental design, data generation, and analysis of single cell RNA sequencing data (primarily generated using the 10x platform) on the command line and within the R statistical programming language. Participants will explore software and protocols, create and modify workflows, and diagnose/treat problematic data utilizing high performance computing services. Exercises will be performed on the command line and within R with a provided dataset. The primary packages used for analysis will be 10x software (for sequence reads to counts) and the R package Seurat for downstream analysis. The final half day will include a seminar and analysis presentation by 10X Genomics (https://www.10xgenomics.com/single-cell/).

 

Registration will be opening very soon!

For more information, go to http://bioinformatics.ucdavis.edu/single-cell-rna-seq-workshop-in-december/.

To subscribe / unsubscribe from the Bioinformatics Core email lists, please follow the instructions at the bottom of http://bioinformatics.ucdavis.edu/contact-us/.

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Upcoming Talks and Events

Events on January 14, 2019
WCMC: Hands-on LC-MS Data processing and Statistics
Starts: 12:00 am
Ends: January 19, 2019 - 12:00 am
Location: UC Davis Conference Center, 550 Alumni Ln, Davis, CA 95616, USA
Description: Registration: http://ucanr.edu/survey/survey.cfm?surveynumber=15575

This course will feature hands-on training with real-world metabolomics data covering LC/MS compound identification, data processing, statistical analysis, network mapping and data interpretation.

We will instruct using a variety of software, workflows, and algorithms but also give theoretical background information and overviews. We will focus on utilizing open source software and only refer to commercial or vendor software when necessary.

All participants will be trained on laptops that were specifically purchased for course training, with all software already installed and data available to use.

The course will include:

untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
The course fees are $ 2,500 per participant to cover expenses for instructors, organization, materials and meals.

more Info:

Jeannette Martins

email: jmartins@ucdavis.edu

phone: +1-530-754-5357

Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.
Events on May 16, 2019
WCMC: Best practice in operating mass spectrometers in Metabolomics
Starts: 12:00 am
Ends: May 20, 2019 - 12:00 am
Location: Genome and Biomedical Sciences Facility, 451 Health Science Dr, Davis, CA 95616, USA
Description: Registration: https://goo.gl/forms/TGeuALrTMfTpGh0O2

This course will enhance your standing and expertise to prepare and successfully run samples in a metabolomic laboratory. It is designed to provide hands-on practical exercises using gas and liquid chromatography coupled to mass spectrometry (GC-MS & LC-MS). The course will focus on untargeted data acquisition in metabolomics with both nominal mass and accurate mass instruments. You will learn how to operate the instruments, how to collect metabolite profiles on complex samples and how to prepare and derivatize samples, troubleshoot instruments, acquire data and perform data quality control routines (QA/QC). Overall, you will receive comprehensive understanding of the current best practices in the metabolomics laboratory.

The course will include:


1. Fundamentals of mass spectrometry, chromatography, and metabolomics.
2. hands-on exercises on sample preparation, including extraction and derivatization
of complex samples for untargeted metabolomics profiling
3. Hands-on exercises to learn how to operate both gas and liquid chromatography
coupled to mass spectrometry (GC-MS & LC-MS).
4. quality control routines (QA/QC) in order to ensure comparable data, reproducibility, and instrument performance.
Events on August 19, 2019
International Summer Sessions in Metabolomics
Starts: 12:00 am
Ends: August 31, 2019 - 12:00 am
Location: UC Davis Alumni Center
Description: Registration: https://docs.google.com/forms/d/e/1FAIpQLSeVnMXxhkMtlET-RGDgW99jA3lr1wS4hypU0kI6O1yGV0GqBg/viewform?usp=sf_link

Contact: Jeannette Martins jmartins@ucdavis.edu

Please, contact us now if you need letters of support to obtain funding from your home institutions.

The West Coast Metabolomics Center organizes an instructional course for researchers for researcher which need a deeper and broader understanding in the field of Metabolomics. This course will span 12 days from August 19-30, 2019.

In order to serve the group interests best and have interesting open discussions we have a small class of 22 participants. The participants come always from all over the world and have a very diverse research background.

The course will include:

study design, including pitfall analysis and hidden biases in studies from microbial, plant, mouse and human cohort research
sample preparation and quality control
in-laboratory detailed discussions standard operating procedures for GC-MS and LC-MS data acquisitions
targeted metabolomics, including monitoring charts and use of isotope labeled internal standards
exercises on flux analysis in cancer cells by isotope tracer analysis
untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
Past course participation:
2018 course: 25 researchers from USA, Brazil, China, Japan, Korea, Taiwan, Russia, Norway, Germany, Poland, Canada
2017 course: 24 researchers from USA, Saudi-Arabia, China, , Korea, Italy, Denmark, Iran, United Kingdom
2016 course: 23 researchers from USA, Saudi-Arabia, China, Thailand, Japan, Italy, Brazil, Chile, Korea, and Canada.
2015 course: 21 researchers from USA, China, Germany, Brazil, Switzerland, Denmark, Canada, Korea, Malaysia, and Netherlands.
2014 course: 20 researchers from USA, New Zealand, Italy, Denmark, China, Canada, Turkey and Switzerland
2013 course: 20 researchers from USA, New Zealand, Costa Rica, Denmark, Luxembourg, Brazil, Columbia, Japan, Korea and Taiwan.
For questions, please contact our program representative Jeannette Martins (jmartins@ucdavis.edu).

Visiting Scientists
Participation in this course is mandatory for visiting international researchers who want to engage in collaborative research projects.
The minimum time span for such collaborative visits is 3 months, preferred is 12 months.
An additional payment of $500 for the visa has to be paid prior to arrival at UC Davis.

Each year, up to five international researchers have started such research visits, funded by agencies in their home countries.
Please contact us at least 6 months in advance to help you with letters of support, booking your course, and obtaining a visa for you.
Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.

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