Research Resource Discovery

Imported Application - IUNI-GUILD Database

Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more.

Matlab R2019a install - requires an **m1.medium** or larger Based on Ubuntu 16.04 LTS Development + GUI support + Docker Installation size ~ 36GB Licensed for: Standard Suite (MATLAB and Simulink) AUTOSAR Blockset Antenna Toolbox Bioinformatics Toolbox Communications Toolbox Control System Toolbox Curve Fitting Toolbox DSP System Toolbox Database Toolbox Datafeed Toolbox Deep Learning Toolbox Econometrics Toolbox Embedded Coder Filter Design HDL Coder Financial Instruments Toolbox Financial Toolbox Fixed-Point Designer Fuzzy Logic Toolbox GPU Coder Global Optimization Toolbox HDL Coder HDL Verifier Image Acquisition Toolbox Image Processing Toolbox Instrument Control Toolbox LTE HDL Toolbox LTE Toolbox MATLAB Coder MATLAB Compiler MATLAB Compiler SDK MATLAB Report Generator Mapping Toolbox Mixed-Signal Blockset Model Predictive Control Toolbox Optimization Toolbox Parallel Computing Toolbox Partial Differential Equation Toolbox Phased Array System Toolbox Powertrain Blockset Predictive Maintenance Toolbox Reinforcement Learning Toolbox Risk Management Toolbox Robotics System Toolbox Robust Control Toolbox Sensor Fusion and Tracking Toolbox SerDes Toolbox Signal Processing Toolbox SimBiology SimEvents Simscape Simscape Driveline Simscape Electrical Simscape Fluids Simscape Multibody Simulink 3D Animation Simulink Check Simulink Code Inspector Simulink Coder Simulink Control Design Simulink Coverage Simulink Design Optimization Simulink Design Verifier Simulink Report Generator Simulink Requirements Simulink Test SoC Blockset Stateflow Statistics and Machine Learning Toolbox Symbolic Math Toolbox System Composer System Identification Toolbox Text Analytics Toolbox Trading Toolbox Vision HDL Toolbox Wavelet Toolbox

This image walks through the steps to search the SRA using the SearhSRA gateway, and set of steps for filtering and visualizing the output generated. This is workflow developed by NCGAS and Rob Edwards with CEWiT REU students. For more information on the developed workflow, the information is available here https://github.com/NCGAS/CEWiT-REU-Identifying-datasets-in-SRA-using-Jetstream

Private, NodeJS which listens data request from app and feed to mongodb. This will be used as pre-processor of the yield meter in bigger cluster.

SMRT Portal and SMRT Analysis

Imported Application - RNA-seq analysis phylogenetics

Imported Application - RNAseq analysis phylogenetics

Has fake planets injected at /findr/Data/fp*

Made Changes the shell script that fetches data from TACC Corral Storage to Jetstream

CAFE (Computational Analysis of gene Family Evolution) is an application that analyzes changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. This image includes a tutorial for a full CAFE pipeline including the applications CAFE, BLAST, MCL and r8s.

This image is the base image for the Frog Call Identification Project in the 2020 Jetstream REU program. It has R, jupyter, sklearn, keras, and vsftpd installed.

Galaxy Standalone - based on Ubuntu 14.04.4 LTS This is a standalone Galaxy server that comes preconfigured with hundreds of tools and commonly used reference datasets: just launch and use. ***It is necessary to launch an instance type of Large or larger.*** See https://galaxyproject.org/cloud/jetstream/ for information about this image and using it.

Genome Analysis Tools Look here of complete list of tools -> https://iujetstream.atlassian.net/wiki/spaces/JWT/pages/334397443/Genomics+Toolkit+image

Anaconda and related packages are installed

Set default python to python 3 and installed pandas, pyspark, matplotlib, pymongo etc

version 2.0

installed jupyterlab, pandas, pyspark, pymongo, and pandas in Python3

InterPro is a database which integrates together predictive information about proteins' function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains

Matlab R2018a with Update 6 built on Ubuntu 18.04 LTS Development + GUI support + Docker Based on Ubuntu cloud image for 18.04 LTS with basic dev tools, GUI/Xfce added Installation size ~ 15 GB -- **requires m1.small or larger** Installation folder: /opt/MATLAB/R2018a Products: MATLAB Bioinformatics Toolbox 4.10 Curve Fitting Toolbox 3.5.7 Database Toolbox 8.1 Econometrics Toolbox 5.0 Financial Toolbox 5.11 Global Optimization Toolbox 3.4.4 Image Processing Toolbox 10.2 Neural Network Toolbox 11.1 Optimization Toolbox 8.1 Parallel Computing Toolbox 6.12 Partial Differential Equation Toolbox 3.0 Statistics and Machine Learning Toolbox 11.3 Symbolic Math Toolbox 8.1 SimuLink is NOT installed!

MongoDB and Node.js on CentOS 7.4 for NoSQL database and back-end service.

Based on the Ubuntu 16_04 Docker image, this image has mysql installed to allow the use of programs such as PASA, OrthoMCL and Trinotate to access database functions.

A version of the Neurepiomics image with data and scripts

To run larger datasets on Photoscan

R, R Studio, and Shiny Server with GCC Shiny port is 3838 - /srv/shiny-server is the data directory Installation size ~ 7.3GB --> an m1.small is now required for proper operation and deployment