Projects and Tutorials

Big Data Analysis Data Integration and Modeling Machine Learning NGS Data RNA-seq

RNA-Seq Data Analysis – Grosmannia clavigera

What is RNA-seq? RNA Sequencing, also known as RNA-seq, is a method for processing Next Generation Sequencing (NGS) data. RNA transcription occurs in an organism when genes are expressed, and the ...

NGS Data RNA-seq

RNA-Seq Data Analysis – Arabidopsis thaliana

  Arabidopsis. is a well studied organism that is often viewed as a model organism in plant biology. Some of it’s important advantages include: -Small size of genome -Short generatio...

Libraries of Small Molecules Structural Biology

Libraries of Small Molecules Analysis

In this Tutorial we’ll be doing a project with Libraries of Small Molecules using the T-BioInfo platform. We’ll be running a Query on a 3d molecule using the mol3 format against PUBC...

Big Data Analysis NGS Data RNA-seq

RNA-Seq Analysis Tutorial – Grosmannia clavigera

After following the steps in the above video, the files used for uploading sample and genome data are referenced by the SVL files contained in this zip: click here to download it. Those steps in...

Big Data Analysis NGS Data RNA-seq

RNA-Seq Analysis with Grosmannia clavigera – Part 1, Background

INTRO T-Bioinfo is a flexible bioinformatics computational system that provides an intuitive and user friendly interface for building pipelines of bioinformatics algorithms for the analysis of big...

NGS Data RNA-seq T-BioInfo Interface

RNA-Seq Analysis with Grosmannia clavigera – Part 2, Process

The first thing we will do as we go about the analysis is look at this section on top. As a default, this section works with an annotated model genome. You will see several options of genomes th...

Big Data Analysis RNA-seq

RNA-Seq Analysis Runthrough – Gene Expression

In this tutorial we’ll be running a One-Button RNA-Seq pipeline. To do this click RNA-Seq, use pre-defined options and then pick your one button, either Gene or Differential Expression. N...

Libraries of Small Molecules Structural Biology

Libraries of Small Molecules Analysis – Curaxin

Cancer cells are able to acquire resistance to therapies with a single target; therefore multitargeted therapies provide the best chance for success for effectively treating cancer. Some conventi...

Big Data Analysis Machine Learning

Data Mining / Post Processing

To use the Data Mining analysis section, the user has to have one or more tables that are in a proper format. It can operate with genomic, transcriptomic, proteomic or metabolomic data that ...

RNA-seq

RNA-Seq – RSEM Simulation

RNA-Seq – RSEM Simulation In RNA-Seq, we can use simulated data, and this video shows how using the rsem-simulate-reads module. In this tutorial we’ll be using the RNA-Seq function ...

ChIP-seq NGS Data

ChIP-Seq Analysis

ChIP-Seq Analysis ChIP-Seq, or chromatin immunoprecipitation sequencing, is a technique that performs analysis of transcriptome data generated by next-generation sequencing technologies or ...

Big Data Analysis ChIP-seq NGS Data

ChIP-Seq Data Analysis – Arabidopsis thaliana

In this tutorial we be using chIP-Seq on the T-BioInfo platform. We’ll be getting out data from a research paper, “Natural variation of H3K27me3 distribution between two Arabidopsis ...

Big Data Analysis Data Integration and Modeling Machine Learning RNA-seq

RNA-SEQ ANALYSIS WITH ARADIOPSIS THALIANA – PART 2, MACHINE LEARNING

For information about how to get to the data needed to run machine learning, please view Part 1. In this video, we go through several types of machine learning options on the T-BioInfo Platform: Qu...

Big Data Analysis RNA-seq

RNA-Seq Analysis with Arabidopsis thaliana - Part 1, Gene Expression

The data referenced in the above video is from GSE57953, and is stored on our server in an error corrected format. The file to upload as NGS data is inside this ZIP file.

T-BioInfo Interface Virology

Virology Analysis Tutorial - Polio with CirSeq

CirSeq is a biological method that was created to look at genetically diverse populations of RNA viruses. This method creates a circularized sequence with tri-repeats of the viral genome. This all...

T-BioInfo Interface

T-BioInfo Interface Overview

When you open the T-BioInfo platform, you will see a list of data types that correlate with different sections of the platform. As an example, we can choose the RNA seq pipeline by clicking on the ...

T-BioInfo Interface Virology

Virology - LayerCake Overview

One of the areas that we’re working in application to Virology is a visual discovery environment that displays the results from data analysis of CirSeq data. If you look here on top, you can ...

RNA-seq

RNA-Seq Educational Project - Whole Transcriptome Profiling of Cancer Tumors in Mouse PDX Models

Whole Transcriptome Profiling of Cancer Tumors in Mouse PDX Models from Tom Koch Download a copy of this presentation. Project Title: Difficulties in Tumor-Stroma Total RNA-seq The “o...

RNA-seq

RNA-Seq Analysis of Macrophages in mouse model Lung Cancer

Pine Biotech - Profiling Tumor-associated Macrophages Using RNA-Seq from Tom Koch Download a copy of this presentation. Project Title: Applying Factor Regression Analysis in a Mouse Model St...