Willi Hennig Society-May 26-31

The Annual Meeting of the Willi Hennig Society will take place May 26-31 at UC Berkeley’s Clark Kerr campus with tours of the natural history museums on campus! Hosted by the BNHM museums of UCMP, MVZ, Essig, and UC & Jepson Herbaria, this conference of Phylogenetics and Evolution has contributed talks and symposia that are aimed broadly and deeply. Visit the meeting website for details and area information. See you there!

 

Update: Letter to Chancellor Christ

Update: Letter to Chancellor Christ

On Wednesday, April 25th, Sara Kahanamoku-Snelling (UCMP graduate student who started the petition) gathered comments from the Change.org petition and sent a more formal letter to Chancellor Christ which you can read below.

As of this writing, Thursday morning, April 26th, there are close to 3,500 signatures on the online petition to show campus administrators the broad support and impact Berkeley Natural History Museums and field stations have had and currently have.

Please keep up the message to Chancellor Christ, Provost Alivisatos, and others that we cannot endure without their support, that dramatic budget cuts on top of the steady erosion of funding jeopardize our traditions and eliminate a critically needed and unique resource for UC Berkeley and most importantly for current and future students.

Letter to Chancellor from students

 

Urgent Petition! Calling all current and former students:

Urgent Petition! Calling all current and former students:

To current and former students of the BNHM, including the UC Botanical Gardens, UC & Jepson Herbaria, Essig Museum of Entomology, UC Museum of Paleontology, Museum of Vertebrate Zoology and the Phoebe Hearst Museum of Anthropology:

The Berkeley Natural History Museums (BNHM) and Field Stations (FS) are currently slated to receive a massive and devastating budget cut in the coming fiscal year. Current students from the BNHM and FS have drafted a petition to the leadership of the university conveying our extreme disappointment in their proposal to endanger the future of ecological, evolutionary, and environmental sciences at Berkeley. Please voice your support by adding your signature to the petition by following this link.

Long-form link: https://www.change.org/p/chancellor-carol-christ-preserve-berkeley-s-museums-and-field-stations

Sara Kahanamoku-Snelling (UCMP graduate student) has kindly set up the petition – all you need to do is sign it!

Spatial phylogenetics of the native California flora

Spatial phylogenetics of the native California flora

A new study, described as “The first “big data” analysis of California’s native plants”, was published by the University and Jepson Herbaria, and available on BMC Evolution. The authors focused on the diversity and endemism in the California flora, applying a novel “spatial phylogenetics” approach that makes it possible to evaluate biodiversity from an evolutionary standpoint, including discovering significant areas of neo- and paleo-endemism. Check out Thornhill, Baldwin, Freyman, Nosratinia, Kling, Morueta-Holme, Madsen, Ackerly, and Mishler 2017 BMC Evolution https://doi.org/10.1186/s12915-017-0435-x

Bioinformatics Workshop coming up!

Bioinformatics Workshop coming up!
A message from  Ke Bi:
Dear Berkeley genomics enthusiasts,
The CGRL will organize two genome assembly workshops next week in 238 Koshland Hall:
 
Part I: Project Design, Sequencing Technologies and Library Methods
 
9/25/2017 (Monday) 1-5pm
 
Part II: Bioinformatics
 
9/26/2017 (Tuesday) 1-5pm 
 
The presenter will be Stefan Prost (stefan.prost@berkeley.edu), previously in the Department of Integrative Biology/Center for Theoretical Evolutionary Genomics and now graciously visiting from Stanford. 
 
Please note that registrations for these two workshops are separate, and you can sign up for either or both. Please go HERE to register for Monday and HERE for Tuesday. For each workshop, space is limited to 30 UCB and affiliate attendees, and registrations are first come first serve.
 

Workshop outline

Whole genome based analyses are becoming increasingly important in biological research, spanning, but not limited to, evolutionary, medical, and conservation contexts. Genome assembly, an initial step in genomic analyses, is a rapidly developing area of research, and so staying up to date with its current state can be challenging. Furthermore, it can be difficult to understand for researchers new to the field. This workshop is targeted towards researchers having anywhere from no background up to advanced knowledge of genome assembly. It will function as a roadmap from designing genome sequencing projects all the way to obtaining a “final”genome assembly, with some brief discussion of downstream analyses. On the first afternoon, I will start very basic by covering pre-planning and laboratory topics such as the different sequencing technologies available, and how to decide on which sequencing platform and library preparation method to use. On the second afternoon, I will outline the different steps needed to process the raw sequencing data, as well as the different assembly, quality assessment and improvement methods. To make the workshop more user-friendly, I will discuss popular tools employed at the different steps.


Part I, 9/25/2017

Basics and A priori Knowledge of the Genome to be Sequenced
Prior knowledge about the genome that will be sequenced can help in choosing the appropriate sequencing and assembly strategy. Here, I will cover some basics and then discuss different genome characteristics that strongly influence whether agenome will be easy or difficult to sequence and assemble successfully.
 
Sequencing Platforms
I will outline different 1st, 2nd and 3rd generation sequencing strategies. The sequencing platforms I will cover in this section include Illumina (MiSeq and HiSeq), IonTorrent, IonProton, ABI Solid, PacBio, Nanopore and Helicos.
 
Sequencing Library Setup
I will discuss the differences (including pros and cons) of Illumina library preparation methods, such as paired-end (PE), mate pair (MP), TrueSeq Synthetic Long-Reads and 10X genomics Linked Long-Reads. In this section, I will also outline other strategies such as BAC or fosmid based sequencing and chromosome folding based long-range linkage methods such as Dovetail Genomics’ Chicago library.
 
 

Part II, 9/26/2017

Raw Read Data Processing
In this section, I will talk about tools used to assess, as well as, improve sequencing read quality.
 
De Novo Assembly Strategies and Tools
To make the workshop more useful, I will outline the different popular assembly tools (for assembly of large genomes) and briefly discuss the underlying algorithms. By doing so, I will also explain terms commonly used in genome assembly  ( e.g. kmer, N50, etc).
 
Assembly Quality Assessment
A critical step after assembling a genome is assessing the quality of the resulting sequence. In cases where different assemblers or different kmer sizes are used, tools are needed to decide which of the assemblies is the best.
 
Bioinformatic Assembly Improvement
There are different tools that can be used to improve a genome sequence after the initial assembly, either by filling gap regions or finding and resolving mis-assembledregions. Furthermore, genome assemblies can be merged to improve quality.
 
Lab-based Assembly Improvement
In this section, I will briefly discuss the pros and cons of Physical and Optical Mapping methods.
 
Draft vs. Finished Assembly
A crucial decision in genomics is whether a genome assembly is good enough to address the desired research questions. Here, I will explain the differences between finished and draft genome assemblies, and give some guidance on deciding if further sequencing is needed or not.
 
Downstream Analyses
To conclude the workshop, I will briefly outline subsequent downstream processing and analyses steps, such as repeat and gene annotation, or how to get a haploid genome sequence into a diploid genome mapping framework.
 

Integrative Biology graduate student teams up with Pixar to tell science stories!

Integrative Biology graduate student teams up with Pixar to tell science stories!

UCMP Grad student Sara ElShafie is highlighted in the Berkeley News for her leadership in teaching scientists to communicate to broader audiences. Her first official workshop was entitled “Science Through Story: Strategies to Engage Any Audience,” in November 2016 at the annual meeting of the Western Society of Naturalists in Monterey, and was a success. It led to a March 2017 workshop at UC Berkeley with industry and faculty participants.

Read about it in the Berkeley News

CalDay 2017

CalDay 2017

CalDay is here!

BNHM has activities and surprises in store; come visit us!

See all that the Berkeley Natural History Museums have to offer

 

Each museum offers something unique:
Visit the Entomology Collection at Essig Museum’s Events

Drop-in learn to be a Maker at the Hearst Museum of Anthropology Workshop

Museum of Vertebrate Zoology (MVZ) Activities – origami, dissections and DNA

Free Shuttle and open house at the UC Botanical Gardens – more information here

Guided tours of the fossils in the Museum of Paleontology (tours every 1/2 hour, free tickets available)

Come prepare plants with UC & Jepson Herbaria and get close with Nature

New video project

New video project

New Videos added featuring the UC&Jepson Herbaria and grad students!

Science In Real Life (IRL) is a YouTube series to show you what being a scientist is like, in real life. Molly Edwards is your tour guide to behind-the-scenes look at the UC & Jepson Herbaria and other spots you find scientists going about their business. She’s engaging and fun to watch, clearly infecting her fellow scientists with a passion to explain and show but never talk down to her audience.

We’ve embedded Part I and Part II of How to make a Herbarium Specimen and All about Herbarium Research with grad students Joyce Chery and Carrie Tribble on a new page What we do. Check out the rest of Science IRL on their Youtube channel.