Bits & Bites

bits_and_bites

 

What is Bits & Bites?

A semi-regular meeting at the Genome Center to discuss bioinformatics, genomics, and all things relating to sequence analysis. As of June 2013, we also hope to start some regular training material about Unix, Perl, and coding in general. We aim to cover a range of basic, intermediate, and advanced material, but we’ll also be encouraging people to bring their own problems to the table.

Who talks at Bits & Bites?

We like to keep things informal and sometimes we just discuss things in a very open manner (while some of us munch on our lunch…hence the ‘Bites’ in Bits & Bites). However, most often one or more people volunteer to lead a discussion on a specific topic and present data and/or slides that will educate the rest of us. These presentations are often short to allow time to discuss things afterwards. Every now and again, we have a speaker from industry or a visiting scholar from another university.

What topics have you discussed?

Some of the previous discussions have concerned: RNA Seq, sequence assembly, SNP calling, use of revision control software, HMMs, sequence alignment, next generation sequencing, large-scale compuing, genome databases, genotyping, working with Illumina data, PacBio sequencing, working with ‘big’ data, advantages/disadvantages of different programming languages.

Who attends?

Grad students, post-docs, project scientists, PIs, and other interested parties.

When do you meet?

Thursdays at 12:00 in room 4202 of the Genome and Biomedical Sciences Facility (map)…but not every Thursday, see next point.

How do I find out more?

Join the (very low-traffic) Bits & Bites mailing list which is mostly used to announce new meetings, but is also a resource in itself (a way of quickly reaching out to other bioinformaticians on campus):

Send an email to sympa@ucdavis.edu. In the subject line of your message, type: subscribe bitsandbites Jim Watson (replace with your name). Leave the message body blank.

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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