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Up Coming Events

NeuroNex DataJoint Training Workshop, April 19-20, 2018

 

Building scientific data pipelines from Python and MATLAB 

In this hands-on workshop, participants will learn to build relational databases to support data pipelines for complex scientific projects using the open-source DataJoint framework. A data pipeline is a sequence of steps (or, more generally, a directed acyclic graph) with integrated data storage and computations at each step. DataJoint pipelines can be created and used from either MATLAB or Python. The workshop will be taught in Python with brief discussions of the MATLAB equivalent. Although DataJoint is a general framework, illustrating examples and worked problems will be based on common neuroscience experiments and recording modalities. We invite scientists who are involved in acquisition, processing, and analysis of data in neuroscience and related fields, particularly those that are part of collaborative projects. Basic knowledge of Python is required for solving exercise problems.

For questions please contact Dimitri Yatsenko.

Day 1
9.00 am – 10.00 am Background and motivation An overview of the challenges around building data pipelines in neuroscience and beyond. Hosting locally and in cloud. Data models and database architectures.

10.10 – 10.40 am Group setup Set up access to JupyterHub and workshop database for use during the workshop.

10.50 am – 11.50 am Getting started with DataJoint Defining a simple data pipeline from scratch in Python. Inserting data into the pipeline and performing basic queries to retrieve data.

11.50 am – 12.40 pm Lunch break

12.40 pm – 2.50 pm Defining computations in a DataJoint pipeline Adding computed tables to the existing pipeline, and automatic population. We will cover data integrity through transactions, distributed computations, and the use of Lookup tables to store computation/analysis parameters.

3.00 pm – 4.00 pm Design patterns and advanced queries Exploration of common design patterns and learn how dependencies (foreign keys) are used to express and enforce relationships and integrity. Visually exploring a pipeline by plotting the entity diagrams. Building more complex queries.

4.10 pm – 4.30 pm Day 1 recap Brief summary of what was covered, and an overview of Day 2 material. References to additional learning resources will be covered.

Day 2
9.00 am – 10.20 am
Case study Part 1: Pipeline design exercises Work with multiple real world experimental and analysis requirements to practice designing and building pipelines.

10.30 am – 11.50 am Case study Part 2: Extending pipelines Work in groups to explore, understand, and extend an existing pipeline with new computations.

11.50 am – 12.40 pm Lunch break

12.40 pm – 1.50 pm Best practices in scientific computations and data sharing Explore tools for sharing code and environments. Discuss best practices in designing and maintaining pipelines in a team of any size.

2.00 pm – 2.30 pm DataJoint roadmap Future developments and available resources.

2.40 – 3.00 pm Workshop recap and concluding remarks Brief summary of the workshop, and open discussion.

BioScience Research Collaborative, 280

  • April 19, 2018 - April 20, 2018
    9:00 am - 3:00 pm

Research Mentor Training for Postdocs

This important workshop is designed to help postdocs develop skills and insight in mentoring young scientists and to provide the opportunity for interactions between mentors at different institutions and in different disciplines.

THIS WORKSHOP IS OPEN TO POSTDOCS ONLY.

 

BioScience Research Collaborative, Event Hall, 6500 Main Street. Spaces are limited.

 

 

 

  • May 2, 2018
    9:30 am - 3:00 pm

NMR and Cell Tracking Symposium, May 16, 2018

Call for abstractsDeadline May 3

Agenda

Confirmed speakers include:

Craig Malloy, UTSW

 

 

Eric Ahrens, UC San Diego

 

Vikas Kundra, MD Anderson Cancer Center

 

 

Vidya Gopalakrishnan, MD Anderson

 

 

Naomi Halas, Rice University

 


Matt Allen, Wayne State University

 

 

Local speakers will discuss current NMR methods and highlight existing resources and technologies available in GCC institutions. Sponsored by the GCC Consortium for Magnetic Resonance.

BioScience Research Collaborative, 6500 Main St., Auditorium

 

Questions contact Suzanne Tomlinson.

  • May 16, 2018
    8:30 am - 5:30 pm

1st Annual GCC Mental Health Research Symposium

Agenda

Call for abstractsdeadline May 7

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

  • May 18, 2018
    9:00 am - 5:00 pm

Reproducible Research (RR) with R and RStudio Workshop, June 6, 2018

First in the series of the GCC Rigor and Reproducibility (RR) Program targeted modules, this workshop will take place in the Bioscience Research Collaborative Room 1003, and will: 1) discuss examples motivating the shift to RR; 2) survey the simple nature of the most common problems; 3) discuss organizing data as projects; 4) use Rstudio, knitr, and rmarkdown to illustrate the use of literate programming to interleave text describing the analyses with the code producing the results; 5) use Rstudio, devtools, and roxygen2 to construct a basic R package; 6) survey other commonly used tools and give pointers to how they might be used and where to   learn more. This course will take place from presumes some working knowledge of R. Attendees are requested to bring laptops with recent versions of R and Rstudio installed, as well as the R packages knitr, rmarkdown, devtools, roxygen2, and RTools (this last is for Windows PCs; it’s required to compile R packages). Limited to the 1st 30 registrants. 

 

BioScience Research Collaborative, Room 1003

  • June 6, 2018
    10:00 am - 2:30 pm

Scientific Data Integrity Workshop, June 13, 2018

Second in the series of the GCC Rigor and Reproducibility (RR) Program targeted modules, this workshop is designed to cover fundamental elements necessary to help assure the quality and integrity of data derived from research studies.  The workshop will review best practices for documentation of research activities, data capture, data (and document) management, and introduce risk mitigation strategies to enhance study reproducibility. A combination of mini lectures, case studies, and group exercises will comprise the activities. Knowledge gained will allow attendees to implement lessons learned within their research environment as elements of a quality system or internal to an individual research project. Limited to the 1st 50 registrants.

 

BioScience Research Collaborative, Room 1003

  • June 13, 2018
    10:00 am - 2:30 pm