At a glance

Where:   The National Center for Genome Resources, Santa Fe, NM

When:    Nov 12-16, 2018 (5 days)

Who:    This program is geared towards undergraduates, graduates and researchers who have minimal or no bioinformatics experience (especially in Differential Gene Expression). Space is limited.

Deadline: 11:59pm Oct. 14 for application submission and unix pre-req completion.

Background: Differential gene expression entails examining the fraction of the genome that is responsible for making products that drive organismal function. Gene expression is influenced by various extrinsic physiological and environmental as well as several intrinsic properties of the organism. Whole transcriptome profiles are becoming increasingly popular and useful and generate large volumes of data. Knowing how to handle and analyze this scale of data and making biological sense is imperative. Gene expression analysis is a valuable skill-set to have and will benefit a large group of researchers with these types of projects.

Objective: During the course of the internship, students will acquire the skill set 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.

Along with UNIX fundamentals, 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.

Tools Covered:  DE analysis: Alignments: STAR and HISAT, read count generation: HTSeq and featureCounts, differential gene expression analysis: DESEQ2, pathway analysis: Cytoscape (ClueGo)

Acceptance (2 parts):

After you hear back that you are a good fit for the internship (acceptance part 1 of 2), you are required to complete a UNIX prerequisite to gain a fundamental understanding of UNIX prior to the course. The course link and instructions are below and you are required to take the test and send a screen shot of your results to This email address is being protected from spambots. You need JavaScript enabled to view it. by 11:59pm Oct. 14th for final acceptance.  You will not be graded - the test signifies completion of the pre-req.

UNIX pre-req training instructions and link

Step 1: Register/Create a free account.
Step 2: Check your email to activate your account.
Step 3: At your Dashboard, click Explore Courses and in the Search box, type "Introduction to Linux" by
LinuxFoundationX. When you're on this page click on this image of the Penguin as shown below.  This will select the FREE course version.  There is another version that has a cost, which you do not want to select.

Step 4: Click Start Course, then click Audit This Course, and then click Resume Course. 
Step 5: Start learning! Focus on chapters 6-10, 12-13, and 15-17 

You can complete the pre-req early (recommended) and send to us as soon as you can prior to 11:59pm Oct. 14th.  This way we can let you know if you've been accepted sooner and you can plan logistics accordingly.

What to Expect Upon Final Acceptance

Plan to prepare a 15-minute PowerPoint presentation about yourself and give the first day of class.  Make sure to cover these areas:

  • What are you currently studying or working on?

  • What are your research interests?

  • How do you plan to apply this workshop material to your area of study?

  • Fun fact about yourself

Have fun with this! We encourage creativity and personality!

Costs and Logistics:

Workshop Rates:

Students and New Mexico Researchers


IDeA Institution Researchers


Academic, Military, Government




Travel and lodging information/costs:

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 of approximately $51.95 per night ($311.70 for 6 nights) 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 food expenses to be $70 - $150.

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.

Application Form: Download and complete Fillable Application Form using Adobe Reader.

Please contact me, 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).