INBRE 2018 Workshops:
Saturday November 3, 10:30-11:45.


Workshop 1 – Leveraging Public Sequence Databases with Next Generation Tools!

Chemistry building, Room 144

Ben Busby, Ph.D., NIH/NLM/NCBI

This workshop will begin with a demonstration of new computational and visualization tools offered by NCBI and others in the bioinformatics community.  Methods for extracting data from databases will also be demonstrated, particularly “edge computing,” or the practice of streaming data from where it is stored rather than downloading it, using magicBLAST as an example. We’ll also discuss other high-throughput ways to access data and metadata, such as the EDirect command line metadata API, taxonomic organization of SRA datasets, and online .bam visualization.  We’ll also discuss how these data extraction mechanisms can be paired with community resources, and general frameworks such as Galaxy, CyVerse, Bioconda, and Bioconductor. Bringing a laptop computer is requested.


Workshop 2 – Preparing for Graduate School

(Chemistry Building, Room 132)

Colin Heyes, PhD, Dept. of Chemistry & Biochemistry, UAF

This workshop is targeted towards under-graduate students who are considering graduate school as a career.  Topics to be discussed will include graduate school expectations and how to prepare for and select the right graduate school and program for you.  A panel of faculty and graduate students will be available to share their tips, strategies, insights, and practical advice.  We conclude with a Question and Answer session, with the possibility of breaking out into smaller groups based on specific interests.


Suresh Kumar, Professor of Chemistry and Biochemistry, UAF

Jessica Pickens, graduate student in Chemistry and Biochemistry, UAF

Perry Caviness, graduate student in Chemistry and Biochemistry, UAF

Doug Rhoads, University professor of Biology and director of the Cell and Molecular Biology (CEMB) program, UAF

Bryce Pelfrey, graduate student in biology, UAF


Workshop 3 – Molecular Modeling

(Chemistry Building Library, Room 225)

Peter Pulay, PhD, Dept. of Chemistry and Biochemistry, UAF

Limited to 12 participants or groups.  If feasible, bring a computer, although this is optional.

Methods of molecular modeling on a per-sonal computer will be addressed, with software available for distribution to up to 12 individuals or cluster teams.


Workshop 4 – Nanochemistry

(Chemistyr Building, Room 147)

Jingyi Chen, PhD, Dept. of Chemistry and Biochemistry, UAF

Limited to 15 participants.

Nanochemistry plays an important role in many applications ranging from medicines to catalysis, electronics, energy conversion and storage. In this workshop, the emphasis focuses on the nano-chemistry in theranostics applications, in particular, the use of nanoparticles in disease diagnostics and therapy. An overview of nanomedicine will be pre-sented, followed by a specific example based on the gold nanostructure nanoplatform.


Workshop 5 A Beginner’s Workshop for Statistical Techniques for Medical Studies

(Gearhart Hall, Room 101)

Zhuoxin Sun, PhD (Senior Statistician, ECOG-ACRIN Cancer Research Group and International Breast Cancer Study Group, Senior Research Scientist, Frontier Science and Technology, Adjunct Associate Professor, Dept. of Math. Science, Univ. of Arkansas)

The workshop has a maximum enrollment of 20.

This workshop will begin with an introduction of some basic ideas about clinical trials in medical research. It will cover different types of clinical trials conducted at various stages of drug development, principles to avoid bias in clinical trials, and ideas about determining the number of patients needed in a clinical trial. Two hands-on case studies with clinical data will be examined to demonstrate how to use some basic statistical techniques in clinical trials. The hand-on exercises will be performed with Microsoft Excel with the Data Analysis Addin.


Workshop 6 – Cellular Mechanisms of Salt and Water Transport in Fish

(Ferritor Building, Room 317)

Christian Tipsmark, PhD, Biological Sciences Department, UAF

The goal of physiological research is to understand the function of living systems from the level of the whole organism and its organs to that of the single cells and bio-molecules.  This workshop highlights mechanisms and regulation of salt and water transport in fish and demonstrates some of the methods used in physiology.  It will cover experimentations with whole animals and isolated tissues.  Techniques demonstrated will include enzyme assays, specific mRNA and protein quantification and cellular localization of specific proteins with immunofluorescence.


Workshop 7 – Physics: “Super-Resolution Fluroescence Microscopy”

(Physics Building, Room 133 and 115A)

Yong Wang, PhD, Physics Dept., UAF

Limited to 15 participants.

This workshop will briefly introduce the basics of super-resolution fluorescence microscopy based on single-molecule localization, which improves the spatial resolution of light microscopy from ~300 nanometers to ~20 nanometers (see 2014 Nobel Prize in Chemistry for more details).  Attendees will have a chance to image an important universal regulatory protein – HNS – in E. coli bacteria, to localize individual HNS molecules, and to produce super-resolved images of HNS proteins in E. coli with a resolution of ~ 20 nanometers.


Workshop 8 – Physics: “High Temperature Superconductor”

(Physics Building, Room 134 and 131)

Jin Hu, PhD, Physics Dept. UAF

The discovery of superconductivity is one of the major breakthroughs in Physics in the last century.  The studies on superconductivity and related phenomena have been awarded several Nobel Prizes.  This workshop will introduce this fascinating quantum phenomenon.  Workshop attendees will then have the opportunity to synthesize the high temperature superconductor.


Workshop 9 – Physics: “A 2D How-to”

(Nano Building, Room 105)

Hugh Churchill, PhD, Physics Dept., UAF

Limited to 15 participants.

After a brief introduction to the field of 2D material research, I will demonstrate the now-famous “Scotch tape technique” that is used to peel apart atomically thin layers of graphene and many other 2D materials from 3D crystals.  Workshop attendees will then have the opportunity to try this themselves using tape, tweezers, and silicon chips, followed by “flake hunting” with a microscope.


Workshop 10 – Physics “Graduate Application”

(Physics Building, Room 132)

Reeta Vyas, PhD, Physics Dept., UAF

Limited to 20 participants.

Participants will learn about career options for physics graduates, dos and don’ts of the application process for Physics Graduate Programs in the US – importance of and preparation for GRE, course work, recommendation letters, assistantships, etc.


Workshop 11 – Visualizing Mitochondrial Dynamics

(Ferritor Building, Room 325)

Shilpa Iyer, PhD, Biological Sciences Dept., UAF

Limited to 10 participants.

The goal is to understand mitochrondrial changes in healthy and diseased states.  We will demonstrate techniques that will visualize and analyze images from multiple cell types corresponding to different mitochondrial diseases.