Free workshop at #UCDavis: “Microbial genomics and transcriptomics hands-on”, Sep 24-25

Was informed of this by Titus Brown, one of the instructors.  Info copied from here.

Microbial genomics and transcriptomics hands-on, Sep 24-25

Who: Ben Johnson (Michigan State University); Tracy Teal (Data Carpentry); C. Titus Brown (UC Davis).

Host: C. Titus Brown

When: Sep 24 and 25, 2015

Times: 9am-3pm on both days

Where: TBD (UC Davis campus).

Cost: there is no fee.

This workshop is open to everyone, including graduate students, postdocs, staff, faculty, and community members. We have extra space for UC Davis VetMed affiliates; contact the host if you are an SVM affiliate.

> Register here <


This two-day hands-on workshop will introduce biologists to microbial genomics and transcriptomics. The primary focus will be on genome assembly and annotation, and subsequent transcriptome analysis, of bacteria.

We will be analyzing a stock data set, and we will be using the Amazon cloud.

Topics overview

  • Logging into the Amazon Cloud
  • Short read quality and trimming
  • Genome assembly (with SPAdes or MEGAHIT)
  • Genome annotation (with Prokka)
  • RNAseq analysis
  • Differential expression analysis

Computer requirements

Attendees will need to bring a computer with a Web browser, an Internet connection, and an ssh client; Windows users should install MobaXterm before the workshop.

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons – 0 License (CC0)fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.

Session on microbial interactions at ASLO 2015 in Spain

Email just received:

Dear colleagues,

This is just to remind you that the deadline for abstract submission (October 10) for the ASLO Aquatic Sciences Meeting in Granada, Spain, 22-27 February 2015 is coming closer. We would like to invite you to participate in our session "MICROBIAL INTERACTIONS ACROSS THE DOMAINS OF LIFE" (# 058). We are looking forward to your contributions on microbial interactions, as well as evolutionary studies related to understanding microbial ecology. Please find more details in the flyer attached.
Feel free to pass this on to other colleagues who might be interested.

Thank you,
Susanne, Valeria & Alex

Deadline for Abstract Submissions: October 10, 2014


Keystone Meeting on the microbiome April 1-6, 2014

Posting this at the request of one of the organizers – Peter Turnbaugh (who as a side note is one of my favorite scientists in human microbiome studies).

Note – The scholarship deadline is a week from Thursday (Dec 5th).

Exploiting and Understanding Chemical Biotransformations in the Human Microbiome

April 1–6, 2014
Big Sky Resort, Big Sky, Montana, USA

Discounted Abstract Deadline: December 5, 2013
Student/Postdoc Scholarship Application Deadline: December 5, 2013 Abstract Deadline: January 9, 2014
Discounted Registration Deadline: February 3, 2014
For more information and to view the full program, visit


BioAgFR 2013 NCBI Discovery Workshops @ UC Davis Library Webinar Edition

>A Fall 2013 Hello to our Library Faculty Representatives to the Shields
>Library Biological & Agricultural Sciences Reference Department.
>Would you please distribute the following email notice to your
>respective departmental email lists, especially those for your graduate
>Thank you!
>The UC Davis Library is pleased to announce:
>2013 NCBI Discovery Workshops @ UC Davis Library [Webinar Edition]
>The workshops will focus on the following areas:
>1. Sequences, Genomes, and Maps: December 17, 2013 from 12:30-2:30pm PT
>2. Proteins, Domains, and Structures: December 18, 2013 from
>12:30-2:30pm PT
>3. NCBI BLAST Services: December 19, 2013 from 12:30-2:30pm PT
>4. Human Variation and Disease Genes: December 20, 2013 from
>12:30-2:30pm PT
>To register:
>You are welcome to register for one or more workshops, each emphasizing
>different sets of NCBI resources. Specific examples will be used to
>highlight important features of the resources and tools under study and
>to demonstrate how to accomplish common tasks.
>Electronic copies of detailed handouts for each session will provide
>step-by-step instructions and additional information about each example.
>All workshops are taught by NCBI staff and will consist of 1.5 hours of
>instruction followed by a Q & A period.
>Due to the US Government sequester, the workshop instructors will not
>be able to present in person at UC Davis, as in previous years.
>Instead, you are invited to attend all sessions via webinar, using your
>own computer or perhaps collaborating with your department or research
>group to view together.
>NCBI Discovery Workshops Website:
>Questions? Contact bioagquestions or

Registration is Open for December Bioinformatics Bootcamps at #UCDavis

Forwarding this …

“Registration is now open for Bioinformatics Bootcamps in December!

We’re excited to announce our next offering of Bioinformatics Bootcamps, which will be held on the UC Davis campus December 10-13.

These focused one-day courses are perfect for the student, postdoc, faculty, or industry professional looking to get up to speed quickly on the latest technologies and techniques in bioinformatics. Students will work on their own laptops and have continued access to software and example data used in the exercises through our public Amazon Web Services virtual machine (details here). The first three bootcamps will use the Galaxy platform, and the final bootcamp will use both Galaxy and the command-line. The Alignment and Assembly bootcamps (Dec. 11th & 12th) require you to know Galaxy, so if you are unfamiliar with Galaxy, you should also take the Introduction bootcamp on Dec. 10th.

Tuesday, December 10:

Introduction to Next-Generation Sequence Analysis with Galaxy

Wednesday, December 11:

Next-Generation Sequence Alignment and Variant Discovery

Thursday, December 12:

Genome Assembly using Next-Generation Sequence Data

Friday, December 13:

Introduction to the Amazon Cloud for Galaxy and the Command-Line

Daily instruction will run from 9am until 5pm. Lunch, light breakfast, and snacks will be provided. Enrollment for each bootcamp will be capped at 24 students. Please enroll early to be assured of a seat, as these bootcamps usually fill up quickly!

More information, including full descriptions of each bootcamp can be found at

Pricing and Payment

The cost for each bootcamp is $200 (academic/government) or $250 (non-academic/industry). We now accept credit cards. UC Davis attendees can also charge their registration directly to a DaFis account.


If you have any questions, please don’t hesitate to contact us:

· Training email:

· Core email:

· Core main telephone line: 530-752-2698

We hope to see you in December!

– The UC Davis Bioinformatics Core Team

Bay Area Malaria Meeting (BAMM) – Tuesday 17 September

Bay Area Malaria Meeting (BAMM)

RSVP by phone: monroe

Come join the ‘updated’ local Malaria Meeting to share your research, policy work, ideas on eliminating malaria, etc. Make your voice heard, network, collaborate and have fun!

Date: Tuesday, September 17th, 2013

Location: Amyris Inc, 5885 Hollis St., Emeryville

Street parking available, accessible by Emery-Go-Round & Amtrak

Time: 6 – 8pm

Format :1- (30 min) Keynote, 2- (15 min) presenters, 30min network

The Key to Malaria Control and Elimination,

Roly Gosling,UCSF- GHG

The Effects of Deforestation and Climate Change on Avian Malaria, Ravinder Seghal, SFSU

Light Refreshments will be served

Sponsored by:

Halophiles 2013 Conference

Forwarding this:

Dear colleague,

You are cordially invited to participate and submit an abstract to the 10th international congress on halophilic microorganisms – Halophiles 2013, which will be held on the campus of the University of Connecticut, Storrs from June 23rd – 27th 2013.

This conference will bring together an exciting cohort of scientists from many fields of halophile research including but not limited to biodiversity, evolution, ecology, astrobiology, biogeochemistry, biochemistry, physiology, protein structure/function, genetics, genomics, metagenomics, and biotechnology.

Please visit our website for more details.

Key Dates:
Deadline for Abstract Submission – April 30th
Deadline for canceling with full refund – May 24th
Deadline for canceling 50% refund – June 7th

Please, kindly forward this invitation to your colleagues.

Thane Papke, Organizing Chairpeson

NCEAS 3-week intensive workshop in ecological analysis and synthesis

Forwarding this email

Hello NCEAS friends,

The National Center for Ecological Analysis and Synthesis (NCEAS) is
pleased to invite applications from early-career researchers for a 3-week
intensive workshop in ecological analysis and synthesis, to take place at
NCEAS in Santa Barbara CA June 19-July 10, 2013.

All travel and living expenses of participants will be covered during the
workshop, thanks to generous support from the Packard Foundation.

Applications are due March 1. For more information and application
instructions, go to:

Save the Date* IOM public workshop on “Microbial Ecology in Health and Disease ” 3/18-19 in DC



The Forum on Microbial Threats is pleased to announce a public workshop on:

Microbial Ecology in States of Health and Disease

March 18-19, 2013

Keck Building, Room 100

500 Fifth St., NW

Washington, DC 20001

Investigations of microbial ecology in a variety of organisms and contexts have begun to illuminate the properties of host-associated microorganisms. These observations have revealed a complex and dynamic network of interactions across the spectrum of “host”, “microbe”, and “environmental” niches that may influence states of health and disease. Alterations in the composition and dynamics of the human microbiota have been associated with a variety of complex diseases –including such chronic conditions as cardiovascular disease, obesity, and the inflammatory bowel diseases. This ‘ecologically’ informed view is a paradigm shift away from the conventional “one-microbe, one-disease” perspective of infection and may lead to new insights for health maintenance, disease prevention, and treatment approaches in humans, animals, and plants.

On March 18 and 19, 2013 the Institute of Medicine’s Forum on Microbial Threats will host a public workshop, in Washington, D.C., to explore the scientific and therapeutic implications of microbial ecology in states of health and disease. Topics to be explored may include: host-microbe interactions in humans, animals, and plants; emerging insights into how microbes may influence the development and maintenance of states of health and disease; the impacts of environmental change(s) on the formation, function, and stability of microbial communities; and research challenges and opportunities for this emerging field of inquiry. This meeting is an update of topics discussed at a 2002 Forum workshop: The infectious etiology of chronic diseases.

The workshop is free and open to the public, but registration is required. A DRAFT Agenda for this meeting is attached for your information.

Click here to register.

Click here for the Meeting Website.

Rediscover the IOM at our new website,

DRAFT AGENDA-March 2013 Microbial Ecology Workshop-012913.pdf