All posts by hollybik

Manuscript preprint now online – Phinch data visualization framework

The preprint for the Phinch software paper is now online (one of my Legacy Eisen Lab projects) Please enjoy the PDF on bioRxiv while we patiently wait for the manuscript to go through the peer review process:

Bik, H.M. and Pitch Interactive (2014) Phinch: An interactive, exploratory data visualization framework for –Omic datasets, bioRxiv, doi: http://dx.doi.org/10.1101/009944

If you’re not familiar with this project – Phinch (http://phinch.org) is an open-source framework for visualizing biological data, funded by a grant from the Alfred P. Sloan foundation. This project has been an interdisciplinary collaboration between researchers (driven by myself at UC Davis) and Pitch Interactive, a data visualization studio in Oakland, CA. If you’re interested in loading up some data in this visualization tool, check out our GitHub wiki for full instructions on preparing files and metadata (if you’re already using the QIIME pipeline, you should be ready to go in ~10 minutes…we tried to make it that easy!)

Environmental Sequencing workshops at #ESA2014

As part of RCN EukHiTS, I’m leading two sessions at the Ecological Society of America 2014 Annual Meeting next month (taking place in Sacramento, August 10-15, 2014) – a Sunday workshop including QIIME and metagenomics tutorials, and a special session (most likely panel discussion) on Monday. I encourage anyone who is interested to register for these events:

Workshops #9884: “Environmental sequencing approaches and computational tools for ecologists” 
Sunday, August 10, 2014
8:00 AM – 5:00 PM

Description: This workshop will bring together an interdisciplinary pool of researchers to discuss current approaches, challenges, and future directions for environmental sequencing studies (-omic studies of bacteria, archaea and microbial eukaryotes). The workshop program will introduce ecologists to common data types and scientific workflows currently employed for the analysis of high-throughput sequencing data (e.g. Illumina/454). Participants will be given overview presentations and hands-on demonstrations for a number of different approaches, including rRNA marker gene analysis, shotgun metagenomics, and metatranscriptomics. This workshop will introduce participants to computational biology tools and software pipelines which can be harnessed for DNA/RNA-based “ecometagenomic” studies. In addition, we aim to solicit feedback from workshop participants, fostering discussions on how to establish better links between traditional ecological research and new, high-throughput sequencing approaches.

Special Sessions #9883: “Ecometagenomics”
Monday, August 11, 2014
10:15 AM – 11:30 AM

Description: The goal of this session is to catalyze cross-disciplinary discussions between the ecology and environmental sequencing communities.  High-throughput sequencing technologies now offer tremendous opportunities to make major inroads into our understanding of global biodiversity and biogeographic patterns. However, in order to make the most of emerging high-throughput sequencing approaches, we must move towards a “systems ecology” mindset, drawing expertise from diverse disciplines. For microbial eukaryotic taxa in particular, we can now conduct en mass biodiversity assessment using traditional loci (rRNA genes) at a fraction of the time and cost required for traditional (morphological) approaches. In addition, as databases of genes with functional descriptions expand, metagenomic approaches become useful for elucidating ecosystem function. Despite this promise, current bottlenecks and roadblocks lie in the development of useful distributed tools, links between molecules and morphology/ecology, and common data standards to allow global comparisons across individual studies. This session will begin with an overview of environmental sequencing approaches, introducing participants to the methods, data types and current advantages and limitations of DNA/RNA-based studies. The session is intended to be highly interactive, including brief talks, moderated discussion points, and solicitation of questions and feedback from audience members. This session would stimulate critical discussion related to the 2014 meeting theme of “Its all ecology.” DNA/RNA-based studies represent an emerging ecological discipline, and as such, it is imperative that the growing community of microbial ecologists begins to build strong links to the traditional ecological research that forms the center point of the ESA meetings.

Another ESA session linked to RCN EukHiTS is oral session OOS10: Ecological Genomics as an Emerging Field: Opportunities for Non-model Organisms (organized by Melis Akman, UC Davis)

Mendeley groups on environmental PCR, metagenomics, and microbial eukaryotes

As part of my NSF Research Coordination Network grant (RCN EukHiTS), I am currently managing a number of Mendeley groups that amalgamate relevant journal articles on different topics related to environmental PCR, metagenomics, and microbial eukaryotes. These groups are open (anyone can join with a Mendeley account), and I’m trying to keep them regularly updated with new articles (Mendeley members can also add articles, which I strongly encourage!):

  • Eukaryotic HTP Studies – Publications relevant to high-throughput environmental sequencing approaches focused on microbial eukaryotes. Articles will include any type of -Omic methods (marker gene amplicons, metagenomics, metatranscriptomics, etc.), eukaryote-focused tools/pipelines, and review/opinion pieces.
  • rRNA in Eukaryotes – Literature related to the ribosomal repeat array in eukaryotic genomes – variation in rRNA gene copy number, intragenomic polymorphisms, concerted evolution, transposable elements and their evolutionary and ecological implications.
  • Environmental PCRs – primer sets and bias – Literature related to primer set usage and bias across all taxonomic groups (bacteria, archaea, fungi and microbial eukaryotes) – includes primer sets and methods focused on 16S, 18S, ITS, other rRNA, COI, and other marker genes used for environmental sequencing.
  • eDNA in aquatic ecosystems – This group focuses on environmental DNA (eDNA) applications in aquatic ecosystems, include use of eDNA in bioassessment and environmental monitoring. Literature collection covers methods, analytical tools, and empirical studies (both basic and applied science).

Using Social Media to Promote Your Research (workshop)

I’ll be running a social media workshop next Friday in the Genome Center – anyone on campus is welcome to attend! Details as follows:

Using Social Media
to Promote Your Research

Friday, February 7, 2014
12:30-2:30pm
Room 4202, Genome Center

Many view social media as either a fun distraction, a waste of time – or both!  But social media tools can be a tremendous resource for academics seeking to share their research, find new collaborations, and ultimately advance their careers.

Attend this workshop to learn how to:

  • Use social media to share and promote your research
  • Identify appropriate audiences and avoid pitfalls
  • Choose the right platforms to help you achieve your goals

Please pre-register using this online form: http://bit.ly/1ajX6Pc (Pre-registration will help to guide the format of the workshop and the type of social media tools covered)

PDF Flyer available here

PacBio Sequence Assembly Workshop

PacBio is hosting an evening symposium next week as part of another workshop I’m organizing on campus. All are encouraged to attend! Plenty of food available afterwards.

PacBio Sequence Assembly Workshop

Tuesday, December 17th 2013, 4 pm – 7 pm

The Auditorium, 1005 GBSF

4:00 pm                     Welcome & Introductions

4:00 – 4:30 pm        Shane Brubaker, Solazymes

“Assembly, haplotyping, and annotation of a high GC algal genome.”

4:30 – 5:00 pm         Jason Chin, PacBio

“String graph assembly for diploid genomes with long reads.”

5:00 – 5:30 pm         Lex Nederbragt, University of Oslo

“Using PacBio reads to improve and validate the assembly of the complex Atlantic cod genome.”

5:30 – 6:00 pm         Lawrence Hon, PacBio

“Larger genome hybrid assembly with PacBio.”

6 pm – 7:00 pm        Reception & Discussions

Light Refreshments Will Be Served in GBSF Lobby

Women in Leadership film series and panel discussion

Just heard about this film series (and ending panel discussion) to take place in the GBSF auditorium this fall – sign up via EventBrite links in this PDF link:

Women in Leadership flyer RSVP

The Women in Leadership Seminar Series will showcase 3 films highlighting gender imbalances around the world—Girl Rising and Half the Sky examined issues like education access for girls and sexual trafficking. To frame the current dialogue about women’s rights in the US, the documentary Makers: Women Who Make America chronicled the past 70 years of women’s pursuit of equality and justice. Inspired to illuminate these issues in the UC Davis community, graduate students Nicole Chaffee and Jeni Lee, with support from Dr. Judith Kjelstrom, designed the Seminar Series to educate, advocate, and inspire our peers to strive toward leadership roles and encourage women in the workplace. The Women in Leadership Seminar Series and Panel could not have been successful without the support of: the UC Davis Biotechnology Program, the Chancellor’s Office, the UC Davis ADVANCE Program, the UC Davis Women’s Resource and Research Center, the UC Davis Office of Campus Community Relations, and the Sacramento Valley Chapter of the Association for Women in Science.

On December 2ndthe series culminates in a Panel Session of extraordinary female leaders from academia, industry, and government, who will discuss the challenges and rewards of being a successful female leader. Our six exceptional panelists are: Linda Katehi, Chancellor, UC Davis; Maureen Stanton, Vice Provost Academic Affairs, UC Davis; Meg Arnold, CEO, Sacramento Area Regional Technology Alliance (SARTA); Constance McKee, CEO, Manzanita Pharmaceuticals; Lois Wolk, Senator, California State Senate; and Michele Wong, CEO, Synergex and CleanWorld.

The overall objective of the Series is to educate, advocate, and inspire women by setting the stage for in-depth discussions regarding issues of equity. Both women and men are encouraged to join in this dialogue about women’s rights, as facilitating meaningful discourse will not only encourage men to embrace their female counterparts as fellow leaders, but importantly, will empower young, bright females to pursue leadership roles. Increasing the number of women in leadership positions will ensure the presence of a female voice and will set positive examples for future generations.

Graduate Student Opportunity in Marine Biology /Environmental Sequencing of micro eukaryotes

Posting a grad student opportunity for a new project I’m involved in – The project will be using high-throughput sequencing techniques to study microbial eukaryotes in Arctic sediments.

Graduate Student Opportunity in Marine Biology / Biological Oceanography
UAF School of Fisheries and Ocean Sciences, Fairbanks, Alaska USA

We are seeking a graduate student research assistant for a project applying high-throughput DNA sequencing techniques in the study of meiofaunal communities in the Arctic. The student will take a lead role in sample processing and data analysis, including both standard microscopic analysis and morphological taxonomy and high-throughput sequencing approaches. Data will be used to assess meiofaunal community structure and diversity in the US Arctic, and identify possible environmental drivers of community structure. Skills developed will include DNA extraction, purification, and next-generation sequencing methods, and analysis of sequence data. Prior experience in molecular methods is desirable, but not essential. The student may also have the opportunity to participate in research cruises in the Arctic.

Prospective students are encouraged to apply at either the MS or PhD level (PhD candidates would be expected to develop additional research objectives that complement the project, and to work with the advisor in pursuing additional funding sources). The position will be based at the University of Alaska, Fairbanks, but the student will be expected to travel for extended periods to University of California, Davis to receive training in sequencing methods and data analysis. Funding is available for 2.5 years, including tuition, stipend (starting at ~$21,000 / year for MS students), and basic health insurance. The successful candidate will be expected to enroll in the graduate program in Spring 2014, but may be hired as a staff research technician as early as Oct. 1, 2013 if available.

To apply:
Application materials and general information about the graduate program are available at http://www.sfos.uaf.edu/prospective/graduate/. Application deadline for spring enrollment is October 15, 2013. Required materials include three letters of recommendation, general GRE scores, and transcripts from all institutions attended. If interested, or for additional information about the project or the position, contact Sarah Hardy (smhardy@alaska.edu) or Holly Bik (hbik@ucdavis.edu).

QIIME workshop at UC Davis (May 2-4, 2013)

UC Davis will be hosting a 2.5 day QIIME workshop following the SMBE Satellite Meeting on Eukaryotic -Omics, running Thursday afternoon May 2nd through Saturday May 4th. Meeting participants and local Bay Area researchers are encouraged to attend.

Due to space constraints, this workshop will be strictly limited to 32 participants.

Click here to complete the application form (form closes March 22, 2013, and this deadline will not be extended)

APRIL WORKSHOP: Phylogenetically correct stats for evolutionary ecologists (RSVP needed)

From CPB Postdoc Luke Mahler:

Dear Davis Ecologists and Evolutionary Biologists,

This Spring Quarter, I’ll be delivering my CPB Postdoctoral Fellowship Workshop, which will be entitled:

“Phylogenetically correct analysis of species data in ecology and evolution”.

This workshop will consist of 3 sessions, to take place over three days:

April 2: 4:10PM-5:30PM (lecture; note this will be the CPB seminar for this week)
April 3: 11:00AM-1:00PM (tutorial 1 – feel free to bring your lunch)
April 4: 1:00PM-3:00PM (tutorial 2)

The format of this workshop will be an introductory lecture followed by two hands-on R tutorials.

In the lecture, which will take place during that week’s CPB seminar slot, my goal is to (1) review why it’s important to account for phylogeny during data analysis, (2) briefly introduce a suite of current methods for doing so, and (3) critically discuss the inherent assumptions and limitations of phylogenetic comparative methods, outlining best practices for conducting basic analyses.

In tutorials, I will lead participants in a series of computer exercises (all in R) designed to provide hands-on experience implementing the most commonly used phylogenetic statistical analyses. In the first tutorial, participants will learn how to prepare and import phylogenetic trees and species data set for analysis, how to visually explore these data, and how to measure phylogenetic signal and select an appropriate model of trait evolution. In the second tutorial, we’ll conduct a number of phylogenetic statistical analyses with a focus on linear models and principal component analysis. We’ll discuss parameter estimation and interpretation under these models, and will cover techniques for assessing sensitivity of results to phylogenetic uncertainty.

The target audience for this workshop are scientists at any stage who are familiar with phylogenetic trees but don’t necessarily have specialized knowledge about how to work with trees when analyzing ecological or other comparative data. No prior experience using R is necessary, although attendees will need to bring their own laptops, and will need to install R in advance of the workshop (it’s free). Attendees do not need to bring data files – we’ll analyze example data sets which I will provide. Faculty, postdocs, and students are all welcome to attend.

If you are interested in attending this workshop, PLEASE CONTACT ME BY EMAILING lmahler@ucdavis.edu. We haven’t decided yet where to hold the workshop – this decision will be based on anticipated attendance. We’ll do our best to secure a room that can accommodate everyone who interested in attending, but can’t guarantee there will be room for you if you don’t let me know in advance.

Thanks, and I hope you can make it.

Best,
Luke Mahler

Center for Population Biology Postdoctoral Fellow
2320 Storer Hall
University of California, Davis
One Shields Avenue
Davis, CA 95616, USA

SMBE Meeting on Eukaryotic -Omics: April 29-May 2 at UC Davis

I’m leading the organization of an SMBE Satellite Meeting focused on Eukaryotic -Omics at UC Davis this spring. The meeting dates have been set as April 29-May 2, 2013, and the meeting description is as follows:

The SMBE Satellite Meeting on Eukaryotic -Omics will bring together an interdisciplinary pool of researchers to discuss current efforts, challenges, and future directions for high-throughput sequencing approaches focused on microbial eukaryotes (environmental studies of non-model organisms). The meeting program will encompass investigations of eukaryote biodiversity, ecology, and evolution, using approaches such as rRNA marker genes, shotgun metagenomics, metatranscriptomics, and computational biology tools and software pipelines.

See the meeting website (http://www.smbe.org/eukaryotes/) for program announcements, registration details, and travel award information. We’re currently in talks to tack on a QIIME workshop at the end of the meeting (tentative dates May 2-4), so keep an eye our for further details. The official conference hashtag will be #SMBEeuks on Twitter.

Our call for travel award applications includes a heavy focus on diversity–encouraging early-career applicants as well as those from underrepresented groups. Please pass on this meeting announcement to anyone who might be interested in attending. Deadline for abstract submission and travel grant applications is Feburary 22, 2013.