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May 16 -19, 2016 | Workshops

WORKSHOPS


--- CAREER SESSION, Monday, May 16, 2016 ---

Career Ready: Elevator Pitch and Interview Skills
Date: Monday, May 16, 2016
Time: 12:30pm - 1:30pm
Location: VC 115
Instructors:
Part 1: Dr. Nana Lee, Director and Lecturer Graduate Professional Development, Faculty of Medicine, University of Toronto
Part 2: Dr. Michael Brudno, Associate Professor & Canada Research Chair in Computational Biology, Hospital for Sick Children and University of Toronto

Description:
Part 1: Improving your elevator pitch. You’ve just bumped into the person who could decide your next career move. They are about to head to their next meeting and you have two minutes to convince them that your science is worthy. Can you do it? In this session you will learn the theory behind how to deliver a great elevator pitch. You will then get the opportunity to put this theory to the test, honing and practicing your pitch with other audience members so that the next time you hop in an elevator, you will be ready.

Part 2: Witness a live interview for a faculty position. Ever wondered what it is like to interview for a faculty position? In this session, you will find out! One brave soul will participate in a “mock” faculty position interview, revealing to the audience the rigors of the interview process. Following the interview, the audience will be asked to participate in a critique of both the interviewee and interviewer.

Postdocs, graduate students and undergraduate students interested in learning communication skills useful for getting a job will benefit form this career session.

Prerequisites: Think about your best 3 line elevator pitch!

GLBIO/CCBC 2016 WORKSHOPS

--- Monday, May 16, 2016 ---


Workshop 1
Microbiome Analysis: 16S and Metagenomics
Date: Monday, May 16, 2016
Time: 10:30am-12:30pm, continuing 1:30pm-3:30pm
Location: VC 213
Instructors: Morgan Langille, Rob Beiko, & Mike Hall (Dalhousie University)

Description: We present a high-level overview of the major steps in analyzing microbiome data including 16S profiling and shotgun metagenomics. In addition, attendees will have hands on time to walk through a tutorial with an example dataset that provides suggestions for best practices in the field.

Prerequisites: Some basic UNIX experience (Newbies can walk through Part 1 and Part 2 of this tutorial: www.dropbox.com/s/9d4q6oxxmg7pq0i/Unix_and_Perl_course.zip?dl=1)

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Workshop 2
Jupyter Notebooks for Performing and Sharing Bioinformatics Analyses
Date: Monday, May 16, 2016
Time:  10:30am-12:30pm
Location:  VC 101
Instructors:  Jonathan Dursi (University of Toronto)

Description:  In this workshop, we will learn:

  • The basics of Jupyter notebooks - what they are and how they work
  • How to install and run Jupyter notebooks on their laptop, in R and Python
  • How to perform interactive analyses in a web browser using Jupyter
  • Using markdown and latex to
  • How to "Port" an R bioinformatics workflow from some scripts into a Jupyter notebook
  • How to share a Jupyter notebook online, using three different approaches


Prerequisites:  Participants will need to have some familiarity with R (or python), and be comfortable entering commands on the command line, but need not be an expert at either

Setup instructions: The data files will be downloaded day of event:

https://github.com/ljdursi/glbio-jupyter-workshop/blob/master/README.md

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Workshop 3
Quick Guide to Best Practices in Software Carpentry
Date: Monday, May 16, 2016
Time:  10:30am-12:30pm, continuing 1:30pm-3:30pm
Location:  VC 215
Instructors:  Marcelo Ponce and Erik Spence (SciNet, U. Toronto)

Description:  At the end of this workshop, participants will be able to put projects under version control with git, and will be able to apply basic best coding practices such as using comments, documentation, and modularization. They will have an overview of other basic software tools that can further improve their productivity. See http://software-carpentry.org/

Scientists at all levels who would like to become more productive by learning (or re-learning) basic computing skills like best practices in coding, version control, and related skills will benefit from this workshop.

Prerequisites:  Some basic command line and python experience will be assumed. Participants should bring a laptop with the following software installed:
1. A linux-like environment
For Windows this could be MobaXTerm (http://mobaxterm.mobatek.net/) or Cygwin (www.cygwin.com/)
2. Python (www.python.org/) or a python Integrated Development Environment such as Enthought Canopy (https://www.enthought.com/products/canopy/) or Anaconda (https://www.continuum.io/downloads),
3. Git (git-scm.com/).

Make sure to do this ahead of time, because there will not be enough time to get this installed on everyone's laptop during the session.

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Workshop 4
Network visualization and analysis with Cytoscape
Date: Monday, May 16, 2016
Time:  1:30pm-3:30pm
Location:  VC 101
Instructors:  Ruth Isserlin, Jeff Liu, Veronique Voisin (Bader lab)

Description:  This workshop will cover general concepts in network visualization and analysis and will teach a pathway enrichment analysis workflow useful for analyzing and interpreting large gene lists from various types of genomics data, including gene expression and genomic mutations.  Scientists at all levels interested in learning the basics of network visualization and analysis with Cytoscape will benefit from this workshop.

Prerequisites:  A laptop with the most recent version of Cytoscape installed (instructions will be provided before the workshop)

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--- Tuesday, May 17, 2016 ---

Workshop 5
Hands-on workshop on Machine Learning with Applications to Bioinformatics

Date: Tuesday, May 17, 2016
Time:  5:30pm-9:30pm
Location:  VC 215
Instructors:  Ivan Kryukov and Jeff Wintersinger

Description:  This workshop will cover how to employ Machine Learning toolbox; including Classification, Clustering, Regression, and Dimensionality Reduction; to explore and analyze biological datasets.

This is an introductory workshop for anyone with basic programming skills who is interested to have a hands-on experience with machine learning techniques.

Prerequisites:  Familiarity with Python; Laptop with Python and scikit-learn
installed. A GitHub page for the workshop with instructions on how to
install necessary packages will be provided prior to the event.

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Workshop 6
Exploring and Refining Core Competencies for Bioinformatics (ISCB Curriculum Task Force)
Date: Tuesday, May 17, 2016
Time:  5:30pm-7pm
Location:  VC 213
Instructors:  Lonnie Welch, Michelle Brazas, Russell Schwartz

Description:  Participants in this workshop will explore the draft competencies and guidelines of the Curriculum Task Force of the ISCB Education Committee, learn how they are being used to shape training programs in different contexts, and work together to provide input into a refined and updated set of core competencies and guidelines.

Prerequisites:  None

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--- Wednesday, May 18, 2016 ---

Workshop 7
Next generation sequencing - From Sample to Sequence
Date: Wednesday, May 18, 2016
Time: 3:30pm-5:30pm
Location: VC 115
Instructor: Adam Rosebrock

>>Sign up here<<

Description: Over the past decade, the development and large-scale deployment of multiple “next generation” technologies has revolutionized the process of sequencing nucleic acids. Since the turn of the millennia, sequencing throughput has evolved from megabases to terabases of information per machine*week and has diversified from one dominant technology to a half-dozen fundamentally different measurement techniques and sample preparation approaches. Although sequence analysis begins for most computational biologists at the common currency of the FASTA/FASTQ file, understanding how these reads were generated is an important part of interpreting sequencing data.

In this two-hour tutorial, I will present the theory and practical considerations of several classic and next-generation sequencing technologies with a specific focus on issues relevant to computational biologists. Participants will gain a mechanistic understanding of next-generation sequencing and biological sample preparation and build a core vocabulary to enable communication across the “wet-dry” divide. Students will be exposed to outstanding problems and caveats of current sequencing approaches and will hopefully be inspired to consider new computational approaches to identify, circumvent, and ultimately correct extant issues with state-of-the-art approaches.

Mirroring how many wet-lab biologists view informatics tools as an impenetrable black box, many computational biologists view sequencing as closed, idealized process. The goal of this session is to provide computational biologists with a working knowledge of the biology and technology underlying sequencing and take the lid off of the black box!

Prerequisites: None

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Workshop 8
Computational approaches to synthetic biology
Date: Thursday, May 19, 2016
Time: 10:30am-12:00pm
Location: VC 115
Instructors: Cathy Su, Esther Jang, Alexander Sullivan (iGEM Toronto)

>>Sign up here<<

Description: iGEM is an international student competition in genetic engineering founded by MIT. Teams of undergraduate and graduate students around the world execute a synthetic biology project of their own design for entry into each year's competition. The power of iGEM lies in that large groups of students simultaneously collaborate. In recent years, more and more students have chosen to incorporate bioinformatics and computational biology into their work. Here we will discuss some examples from previous projects and why bioinformatics has been valuable, then consider what the future work of iGEM may bring to the field.

Prerequisites: None

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