Bioinformatics for RNA-Seq - 2 Day Workshop

This is a two day workshop that will run both Monday, April 1 AND Tuesday, April 2 from 9 am - 12 pm. Please bring your own computer.

High throughput RNA sequencing allows genome-wide investigation of gene expression and regulation. However, designing an experiment and choosing the right tools for analysis can be challenging. This two-day course aims to teach the basics of obtaining and analyzing RNA-seq data: Experiment design, quality control, alignment and visualization of reads and differential expression analysis. Analysis will be done with tools available on the Tufts High Performance Compute Cluster and example code and tutorials will be available at https://sites.tufts.edu/biotools/tutorials/.

Location: 
SEC 117
Date: 
Monday, April 1, 2019 - 9:00am to 12:00pm
Data Lab Instructor: 
Rebecca Batorsky

Today's
Hours

10:00am - 9:00pm

Workshops This Month And Beyond

All Workshops

Thursday, January 24, 2019 - 1:30pm to 3:00pm
Location: CLIC 114

This is designed to be an introductory level workshop on Basic Linux (the command line environment and some useful commands).

**Required** This is a hands-on workshop and we will be using Tufts HPC cluster for demonstration purposes. If you don't already have access to Tufts HPC cluster, please go to https://research.uit.tufts.edu/ and fill out the "Request account for Research Computing Cluster" Form at least 2 days before the workshop.

No previous Linux experience is required.

**Required** Please bring your own laptop!

Friday, January 25, 2019 - 10:30am to 11:30am
Location: Tisch Library 223

Interested in getting started with data analysis, coding, or just want to get more comfortable with your computer? Join us for a gentle introduction to the tools available for different tasks you might be learning about. This session will have no prerequisites or expected knowledge – show up as you are and feel comfortable asking whatever questions you have.

Monday, January 28, 2019 - 11:00am to 12:30pm
Location: Tisch Library, Data Lab, Room 203

Interested in learning the basics of Geographic Information Systems (GIS), but couldn’t get into the class? Come join us for a quick workshop and learn the basics of adding and symbologizing data, querying attribute tables, and creating a final map product for publication using ESRI ArcMap.

Wednesday, January 30, 2019 - 10:30am to 11:30am
Location: Tisch Library, Data Lab, Room 203

This workshop is designed to get you started with the statistical programming language R. We provide an overview of the R language along with the RStudio interface. During the session, we use datasets built into RStudio to introduce importing data, performing descriptive statistics and making simple visualizations to get you familiar with working in R. This workshop is suitable for those who have not worked with R/RStudio before. No previous statistical experience is required for this session.

Thursday, January 31, 2019 - 1:30pm to 3:00pm
Location: CLIC 114

This workshop is a breif introduction of the structure of the Tufts HPC cluster, as well as the basic usage of it's scheduler "SLURM". 

**Required** This is a hands-on workshop and we will be using Tufts HPC cluster for demonstration purposes and practices. If you don't already have access to Tufts HPC cluster, please go to https://research.uit.tufts.edu/ and fill out the "Request account for Research Computing Cluster" Form at least 2 days before the workshop.

Basic Linux knowledge is required. If you are not familiar with Linux, please check out our "Introduction to Basic Linux Workshop".

**Required** Please bring your own laptop!

Monday, February 4, 2019 - 10:00am to 11:00am
Location: Tisch Library, Data Lab, Room 203

We all have a growing collection of digital files – documents and notes, data files, charts and graphs, pictures… the list is endless! In this workshop we will talk about strategies and tools that you can use to keep track of all of your work so that your files are easy to find and safe.

Thursday, February 7, 2019 - 10:30am to 11:30am
Location: Tisch Library, Data Lab, Room 203

This workshop is designed to get you familiar with the Stata. We provide an overview of Stata interface and basic functions. During the session, we introduce some descriptive statistics commands and recoding commands to help you gain familiarity with Stata syntax. This workshop is suitable for those who have not worked with Stata before or those seeking a refresher session.

Thursday, February 7, 2019 - 1:30pm to 3:00pm
Location: CLIC 114

This is designed to be an introductory level workshop on Basic Linux (the command line environment and some useful commands).

**Required** This is a hands-on workshop and we will be using Tufts HPC cluster for demonstration purposes. If you don't already have access to Tufts HPC cluster, please go to https://research.uit.tufts.edu/ and fill out the "Request account for Research Computing Cluster" Form at least 2 days before the workshop.

No previous Linux experience is required.

**Required** Please bring your own laptop!

Monday, February 11, 2019 - 11:00am to 12:00pm
Location: Tisch Library, Data Lab, Room 203

You’ve heard of close reading, but how about distant reading? Want to learn how to visualize thematic patterns across Shakespeare’s plays? Presidential speeches? Newspaper articles? Thousands or millions of texts? This workshop will provide an introduction to some simple, free web-based tools for text analysis and visualizations that you can bring into your research and classes. No programming experience required.

Tuesday, February 12, 2019 - 10:30am to 12:00pm
Location: Tisch Library 223

You have a right to exist safely in digital spaces. Although we have to rely on outside parties for technology to access these spaces, there are tons of helpful tools and strategies that allow you to take greater control of your digital life and mitigate the risk of malicious threats. During this workshop, we’ll walk through common areas of digital life such as web browsing, private data, and smartphones to show you different ways that you can implement as much or little security as you’re comfortable with. Thanks to Hack*Blossom's DIY Guide to Feminist Cybersecurity for this workshop description!

Thursday, February 14, 2019 - 1:30pm to 3:00pm
Location: CLIC 114

This workshop is a breif introduction of the structure of the Tufts HPC cluster, as well as the basic usage of it's scheduler "SLURM". 

**Required** This is a hands-on workshop and we will be using Tufts HPC cluster for demonstration purposes and practices. If you don't already have access to Tufts HPC cluster, please go to https://research.uit.tufts.edu/ and fill out the "Request account for Research Computing Cluster" Form at least 2 days before the workshop.

Basic Linux knowledge is required. If you are not familiar with Linux, please check out our "Introduction to Basic Linux Workshop".

**Required** Please bring your own laptop!

Wednesday, February 20, 2019 - 10:00am to 11:00am
Location: Tisch Library, Data Lab, Room 203

In today’s day in age, static paper maps can only get you so far. Online web-maps allow viewers to engage with spatial data in an interactive manner, allowing for more in depth analysis and storytelling. In this introductory workshop, we will learn how to use ArcGIS Online to add layers to the map, configure pop-ups to make your map features informative, and present your map with a finished look and a nice user experience for mobile applications or embedding into websites.

Friday, February 22, 2019 - 1:00pm to 2:00pm
Location: Tisch Library, Data Lab, Room 203

So you found a dataset, but it doesn’t quite work for you; now what? Never fear! We have lots of tips and tricks that you can use to clean up a messy data set, adjust the data to line up with what you already have, or just reduce the size of the dataset to only include what you need. We will look at how you can use Excel and OpenRefine to evaluate and work with your data.

Monday, February 25, 2019 - 12:00pm to 1:00pm
Location: Tisch Library, Data Lab, Room 203

Wouldn’t it be great if ArcMap was less expensive, open source, and more versatile? Never fear, QGIS is here! QGIS is a free, open-source software that allows you to create, edit, visualize, analyze and publish geospatial information on Windows, Mac, and Linux platforms. This workshop will cover introductory GIS concepts using QGIS. In this intro workshop, you’ll learn how to stylize layers, make selections, set your projection, and create a final map composition in QGIS.

Tuesday, February 26, 2019 - 12:00pm to 1:30pm
Location: Tisch Digital Design Studio (DDS)

In this workshop you will learn recording tools and strategies to build a short project through exploratory listening. We will use GarageBand but skills are translatable to software such as Audition, ProTools or Logic. We will cover basic media management, starting a new project, importing, editing techniques, and exporting. Demo media will be provided. 

Wednesday, February 27, 2019 - 10:00am to 12:00pm
Location: Tisch Library 223

Join Digital Collection and Archives (DCA) staff to learn how to use a tool developed by Stanford, ePADD, to easily conduct research in email collections held by DCA and other archival repositories. You will also learn how you can use ePADD to save, organize, find, and perhaps eventually donate your own email to an archives.

Friday, March 1, 2019 - 2:00pm to 3:00pm
Location: Tisch Library, Data Lab, Room 203

Description Pending

Tuesday, March 5, 2019 - 10:30am to 11:30am
Location: Tisch Library, Data Lab, Room 203

Interested in exploring an online tool for simple, collaborative scientific and technical writing? Learn how to use Overleaf to make the process of writing, collaborating, and publishing scientific documents in LaTeX quicker and easier. Overleaf is a browser-based editor that allows direct code editing and a Rich Text formatter that does the work for you. Collaborate with colleagues, find templates for major journals, and format bibliographies.

Thursday, March 7, 2019 - 11:00am to 12:00pm
Location: Tisch Library 223

Are you planning to incorporate images, text, data, or other material created by someone else into a project, and wondering what’s allowed? Are you interested in learning more about your rights to your own work? This workshop will provide an introduction to copyright, Fair Use, and licenses in order to facilitate creating and sharing your project.

Tuesday, March 12, 2019 - 1:00pm to 2:30pm
Location: Tisch Library 223

Creating a website to showcase your research interests and outputs is one of the most powerful ways you can establish yourself in your field. During this workshop, you will become familiar with GitHub Pages, a super easy—and super sustainable—platform for developing your scholarly online presence.

Wednesday, March 13, 2019 - 10:00am to 11:30am
Location: Tisch Library, Data Lab, Room 203

GPS is changing the way users collect and manage geographic data. From handheld units to smart phones, GPS units make it extremely convenient to record locations in the field while simultaneously collecting survey information (e.g. water quality data, questionnaire responses, etc).  In this workshop, students will learn how to prepare a field data collection sheet, use Garmin GPS units to collect data, download the data and join survey responses, and import the results into Google Earth and Google Maps.  No GIS experience required.

Wednesday, March 27, 2019 - 10:00am to 11:30am
Location: Tisch Library, Data Lab, Room 203

Designed to replace paper notebooks, a LabArchives Digital Notebook can be used to document ideas, notes, research, experiments, and procedures. They are designed for intuitive use, ease of search, copying and versioning. They support collaboration with many users and includes access controls. In this workshop you will be provided an overview of the LabArchives Digital Research Notebooks. We will go over the feature tools and show you the benefits of moving from a paper to a Digital Notebook.

Computers will be provide during the training session but feel free to use your laptop. And your Tufts account is required to log into the LabArchives Digital Notebook solution.

Wednesday, March 27, 2019 - 11:30am to 1:00pm
Location: Tisch Library, Data Lab, Room 203

In this workshop, we will explore advance sharing with group management and widgets to create customized forms for data entry. Focused items are creation of research group specific forms and database for Chemical Inventory and Freezer Box.

Computers will be provide during the training session but feel free to use your laptop. And your Tufts account is required to log into the LabArchives Digital Notebook solution.

Wednesday, March 27, 2019 - 3:00pm to 4:00pm
Location: Tisch Library, Data Lab, Room 203

Charts, graphs, maps, and infographics are a great way to communicate research, but not all visualizations are created equal. In this workshop we will talk about the ways that you can create truthful and effective visualizations and look at a series of examples to see how visualizations can go terribly wrong. We will also start to work with Tableau to make attractive visualizations.

Thursday, March 28, 2019 - 1:30pm to 3:00pm
Location: CLIC 114

This is designed to be an introductory level workshop on Basic Linux (the command line environment and some useful commands).

**Required** This is a hands-on workshop and we will be using Tufts HPC cluster for demonstration purposes. If you don't already have access to Tufts HPC cluster, please go to https://research.uit.tufts.edu/ and fill out the "Request account for Research Computing Cluster" Form at least 2 days before the workshop.

No previous Linux experience is required.

**Required** Please bring your own laptop!

Friday, March 29, 2019 - 2:00pm to 3:00pm
Location: Tisch Library, Data Lab, Room 203

Just when you finally get ArcMap down, they develop a new platform for ArcGIS! A new ribbon based and map centric product, ArcGIS Pro has all the tools you’ve come to know and love, plus it’s easier to use than ArcMap (once you get used to it). Come learn the future ESRI… you might like it more than you think!

Monday, April 1, 2019 - 9:00am to 12:00pm
Location: SEC 117

This is a two day workshop that will run both Monday, April 1 AND Tuesday, April 2 from 9 am - 12 pm. Please bring your own computer.

High throughput RNA sequencing allows genome-wide investigation of gene expression and regulation. However, designing an experiment and choosing the right tools for analysis can be challenging. This two-day course aims to teach the basics of obtaining and analyzing RNA-seq data: Experiment design, quality control, alignment and visualization of reads and differential expression analysis. Analysis will be done with tools available on the Tufts High Performance Compute Cluster and example code and tutorials will be available at https://sites.tufts.edu/biotools/tutorials/.

Wednesday, April 3, 2019 - 10:30am to 12:00pm
Location: Tisch Library, Data Lab, Room 203

This is a hands-on workshop designed to get you started analyzing data using Python and Jupyter Notebooks. We will provide a whirlwind overview of what Python is (and isn't) and why you might want to use it to look at your data. Then we'll dive into some programming basics and discuss:

  • What are variables and how do I use them?
  • What other data structures are available?
  • Essential Python packages for data analysis (NumPy, Matplotlib, Pandas, and more) and how to import them
  • The basics of visualization with Matplotlib
  • How do I import my data?

No previous programming experience is required for this workshop, and computers will be provided through the Data Lab. If you already have some data that you would like to explore, there will be time to do so at the end, so please feel free to bring it along (preferably in Excel or CSV format). Sample datasets will also be provided.

Thursday, April 4, 2019 - 1:30pm to 3:00pm
Location: CLIC 114

This workshop is a breif introduction of the structure of the Tufts HPC cluster, as well as the basic usage of it's scheduler "SLURM". 

**Required** This is a hands-on workshop and we will be using Tufts HPC cluster for demonstration purposes and practices. If you don't already have access to Tufts HPC cluster, please go to https://research.uit.tufts.edu/ and fill out the "Request account for Research Computing Cluster" Form at least 2 days before the workshop.

Basic Linux knowledge is required. If you are not familiar with Linux, please check out our "Introduction to Basic Linux Workshop".

**Required** Please bring your own laptop!

Friday, April 5, 2019 - 1:00pm to 2:00pm
Location: Tisch Library, Data Lab, Room 203

Charts, graphs, maps, and infographics are a great way to communicate research, but not all visualizations are created equal. In this workshop we will talk about the ways that you can create truthful and effective visualizations and look at a series of examples to see how visualizations can go terribly wrong. We will also start to work with Tableau to make attractive visualizations.

Monday, April 8, 2019 - 10:00am to 11:00am
Location: Tisch Library, Data Lab, Room 203

Description Pending

Wednesday, April 10, 2019 - 1:00pm to 2:30pm
Location: Tisch Digital Design Studio (DDS)

In this workshop you will learn editing tools and strategies using found media with the aim of understanding different ways one could approach the footage. We will cover media management, starting a new project, importing, editing techniques, and exporting. Demo media will be provided. 

Thursday, April 11, 2019 - 1:30pm to 3:00pm
Location: CLIC 114

This is designed to be an introductory level workshop on Basic Linux (the command line environment and some useful commands).

**Required** This is a hands-on workshop and we will be using Tufts HPC cluster for demonstration purposes. If you don't already have access to Tufts HPC cluster, please go to https://research.uit.tufts.edu/ and fill out the "Request account for Research Computing Cluster" Form at least 2 days before the workshop.

No previous Linux experience is required.

**Required** Please bring your own laptop!

Friday, April 12, 2019 - 2:00pm to 3:00pm
Location: Tisch Library, Data Lab, Room 203

 Description Pending

Wednesday, April 17, 2019 - 3:00pm to 4:00pm
Location: Tisch Library, Data Lab, Room 203

Data is an essential part of your research, but keeping track of it can be tricky and data management plans are an increasingly important component of project planning. In this workshop we will talk about the tools and strategies that you can use to manage your data from collection all the way through to when you want to put it somewhere to be preserved.

Thursday, April 18, 2019 - 10:30am to 11:30am
Location: Tisch Digital Design Studio (DDS)

An interactive session on elements and principles of poster design. While these principles are applicable regardless of what software you design in (or even non-digital design), we’ll make use of the easy to use, free web-based application Canva.

Thursday, April 18, 2019 - 1:30pm to 3:00pm
Location: CLIC 114

This workshop is a breif introduction of the structure of the Tufts HPC cluster, as well as the basic usage of it's scheduler "SLURM". 

**Required** This is a hands-on workshop and we will be using Tufts HPC cluster for demonstration purposes and practices. If you don't already have access to Tufts HPC cluster, please go to https://research.uit.tufts.edu/ and fill out the "Request account for Research Computing Cluster" Form at least 2 days before the workshop.

Basic Linux knowledge is required. If you are not familiar with Linux, please check out our "Introduction to Basic Linux Workshop".

**Required** Please bring your own laptop!

Friday, April 19, 2019 - 2:00pm to 3:00pm
Location: Tisch Library, Data Lab, Room 203

Sick of using only PowerPoint to make presentations? Esri Story Maps are web applications that let authors combine beautiful, interactive maps with narrative text, striking images, and multimedia including video. Impress your professors, bosses or friends with these attractive and easy to use applications while bringing your story to life. Story maps can be embedded in web pages and truly up your presentation game!