Where

The National Center for Genome Resources (NCGR), Santa Fe, NM

When

July 1 - 26, 2019 (4 weeks)

Audience

This program is geared towards training biologists (undergraduates, graduates and researchers) with minimal or no bioinformatics experience. Space is limited. 

Background

The main goal of this bioinformatics course is to introduce various tools and methods to analyze next generation data to the enrolled participants. With the explosion in data generation, it is imperative to utilize effective bioinformatics techniques in the UNIX platform and expose students to the approaches currently used to tackle data of this scale.   

Objectives

During the course of the internship, students will acquire the skillset to independently analyze their own dataset. They will firstly be introduced to fundamentals of UNIX followed by in-depth concepts, workflows and most current tools used for analysis.  This course is geared towards training biologists and the lectures are tailored for biologists. 

Planned topics:

  • Assembly methods with QC, assembly generation with short and long read, hybrid assemblies and transcriptome assemblies
  • DNA-Seq variant calling analysis with alignment, variant calling, and variant filtering.
  • RNA-seq and differential gene expression analysis including QC, alignments, read count generation and differential gene expression analysis. Post DE analysis, pathway analysis will be taught.
  • Metagenomics/16S (community analysis)
  • Visualization session will cover generation of simple graphs using R and browsing through genome browsers such as IGV.

Workshop Rates

New Mexico Students & Researchers Free
All Other Students $1,750
IDeA Researchers $2,000
Academic, Military, Government $2,500
Commercial $3,000

 

Lodging scholarships  (for NM-INBRE students only)

If you are not an NM-INBRE student, check to see if you are from an INBRE funded state, here. If so, connect with your local INBRE Administrative Core to see if funding is available to support your educational pursuit by attending our workshop.

Application Packet due 11:59pm May 15, 2019 (MST)

  1. Application Form: Download and complete Fillable Application Form using Adobe Acrobat or Adobe Reader.
  2. UNIX prerequisite:  Please thoroughly review the following to gain a fundamental understanding of UNIX prior to the course. Indicate this has been completed on Application Form.
    1. Review Introduction to the UNIX Operating System and Tutorials 1 – 4 http://www.ee.surrey.ac.uk/Teaching/Unix/
    2. Review vi editor https://www.cs.colostate.edu/helpdocs/vi.html 

Late applications will not be accepted.  Selection Committee to select interns shortly after application deadline. If there are any questions while reviewing your application packet, a phone conversation may be required. 

What to expect upon acceptance

  1. Email confirming acceptance into the internship program.
  2. Dataset (if applicable) to be sent to Project Coordinator, Lisana Chavez by June 5, 2019.

Travel & Lodging Information

Travel to and from Santa Fe, NM   The Santa Fe Regional Airport is approximately 7 miles away (15 minute drive to the hotel) and Albuquerque International Sunport is approximately 60 miles away (1 hour drive to the hotel).   Santa Fe airport is very convenient.

Lodging at Santa Fe Suites  To be coordinated through Project Coordinator at the special student rate ($1,301.40 total including taxes) for a single queen room.  Just around the corner from the Santa Fe Suites is an Albertson's supermarket where students may purchase groceries.  Also, there are a number of restaurants in the area (sandwiches, Chinese food, pizza, etc.).  Additionally, the hotel serves a free continental breakfast each morning.  Santa Fe Suites is approximately ½ mile away and a 15-minute walk to NCGR.  NCGR staff can always lend a hand with transportation to and from Santa Fe Suites if needed (e.g. inclement weather) as well. 

Food   The hotel serves a free continental breakfast each morning and we will occasionally organize lunch outings at local Santa Fe eateries as a group (optional).  Santa Fe has excellent food—we are known for our green and red chiles!  We estimate total food expenses to be approximately $350 (if $12.50/day).

Public transportation   Available if needed. There is a city bus stop 400 ft from NCGR and the Zia train station approximately ¼ mile from Santa Fe Suites.  These can be used to visit downtown Santa Fe, sightseeing or other destinations.

 

Contact

Please contact Project Coordinator, Lisana Chavez, with any additional questions you may have at This email address is being protected from spambots. You need JavaScript enabled to view it. and we look forward to your participation!

 

Sponsored by New Mexico IDeA Network for Biomedical Research Excellence (NM-INBRE).