LibGuides: Engineering & Innovation: Data Science

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Data Science Learning Tools

ActiveWizards Case Studies
ActiveWizards is a team of experienced data scientists and engineers focused on complex data projects. We provide high-quality data science, machine learning, data visualizations, and big data applications services.
The Carpentries
The Carpentries project comprises the Software Carpentry, Data Carpentry, and Library Carpentry communities of Instructors, Trainers, Maintainers, helpers, and supporters who share a mission to teach foundational computational and data science skills to researchers. We collaboratively develop openly-available lessons and deliver these lessons using evidence-based teaching practices. We focus on people conducting and supporting research.
DataCamp
Sign up for a free account to find interactive tools for learning data analysis and R at your own pace.
HSRIC (archived)
Health Services Research Information Central from NIH links to a selective representation of health services resources for data.

Data Analysis Tools & Tutorials

Atlas.ti
A tutorial to get started with the computer assisted qualitative data analysis software (CAQDAS) program ATLAS.ti.
Cytoscape
Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. Download it here. Cytoscape has apps available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.
RStudio
RStudio develops free and open tools for R and enterprise-ready professional products for teams to scale and share work.

SAS
This guide provides a general overview of the SAS statistical software suite.
SPSS Tutorial
This guide provides a general walkthrough of SPSS's basic features.

Coding & Development Tools

Apache Airflow
Use airflow to author workflows as directed acyclic graphs (DAGs) of tasks. The airflow scheduler executes your tasks on an array of workers while following the specified dependencies. Rich command line utilities make performing complex surgeries on DAGs a snap. The rich user interface makes it easy to visualize pipelines running in production, monitor progress, and troubleshoot issues when needed.
Black
Black makes code review faster by producing the smallest diffs possible. Blackened code looks the same regardless of the project you’re reading. Formatting becomes transparent after a while and you can focus on the content instead.
CircleCI
CircleCI automatically runs your build in a clean container or virtual machine, allowing you to test every commit. CircleCI integrates with GitHub, GitHub Enterprise, and Bitbucket.
Colaboratory (Google)
Colaboratory, or "Colab" for short, allows you to write and execute Python in your browser, with:
- Zero configuration required
- Free access to GPUs
- Easy sharing
DVC
Open-source Version Control System for Machine Learning Projects
Flake8
Flake8 is a wrapper around these tools: PyFlakes; pycodestyle; Ned Batchelder’s McCabe script. Flake8 runs all the tools by launching the single flake8 command. It displays the warnings in a per-file, merged output.
Jupyter
Jupyter supports interactive data science and scientific computing across all programming languages. Jupyter Notebook and its flexible interface extends the notebook beyond code to visualization, multimedia, collaboration, and more.
Luigi
Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built in.
Pep 8 - Style Guide for Python Code
This document gives coding conventions for the Python code comprising the standard library in the main Python distribution. Please see the companion informational PEP describing style guidelines for the C code in the C implementation of Python [1]. This document and PEP 257 (Docstring Conventions) were adapted from Guido's original Python Style Guide essay, with some additions from Barry's style guide [2].
PyCharm
PyCharm knows everything about your code. Rely on it for intelligent code completion, on-the-fly error checking and quick-fixes, easy project navigation, and much more.
Pytest
Pytest is a mature full-featured Python testing tool that helps you write better programs. The pytest framework makes it easy to write small tests, yet scales to support complex functional testing for applications and libraries.
RunMyCode
To allow researchers to quickly disseminate the results of their research. This will considerably increase the potential of citations of scientific papers. To provide a large community of users with the ability to use the latest scientific methods. This will speed up the process of converting scientific results into productive forces. To allow members of the academic community (researchers, editors, referees, etc.) to replicate scientific results and to demonstrate their robustness. This will increase transparency and trust in science.
Travis CI
The simplest way to test and deploy your projects. Easily sync your GitHub projects with Travis CI and you'll be testing your code in minutes.
Visual Studio Code
Visual Studio Code is a lightweight but powerful source code editor which runs on your desktop and is available for Windows, macOS and Linux. It comes with built-in support for JavaScript, TypeScript and Node.js and has a rich ecosystem of extensions for other languages (such as C++, C#, Java, Python, PHP, Go) and runtimes (such as .NET and Unity).

Data Resources from NIH and NLM

Big Data to Knowledge Program Resources
The Big Data to Knowledge (BD2K) Centers of Excellence have developed new approaches, methods, software tools and related resources including publications, data standards, and educational resources to advance Big Data Science in their relevant biomedical area of focus.
Data Literacy & Management (archived)
From Health Services Research Information Central (HSRIC) - The information on this page is intended to serve as an introduction to the topics of data science, data literacy, data management, data sharing, and research reproducibility. Though the emphasis is on health data, information from the broad data science community is included.
NIH Data Sharing Policy
NIH has issued a new Final NIH Policy for Data Management and Sharing, which will require NIH funded researchers to prospectively submit a plan outlining how scientific data from their research will be managed and shared. On January 25, 2023, the new policy will come into effect and replace the 2003 NIH Data Sharing Policy currently in effect.
NNLM RD3
NNLM RD3: Resources for Data-Driven Discovery has been developed to foster learning and collaboration in data science. In order to support sharing, curating, and annotating biomedical data, NNLM RD3 serves as a resource for librarians, library students, information professionals, and interested individuals to learn about and discuss: library roles in data science; fundamentals of domain sciences; emerging trends in supporting biomedical research.

Clinical Data Research Networks

HMO Research Network
The HCSRN brings together the research centers from many of the nation's best and most innovative health care systems. Collectively, the HCSRN represents more than 2,000 scientists and research staff with methodological and content expertise from an array of disciplines such as epidemiology, economics, disparities, outcomes and quality assessment, clinical trials, and genomics.
FDA Mini-Sentinel Network
Safety surveillance of medications.
PCORnet
Clinical data research networks; common data model for subset of data.

General Data Repositories

CDC Data & Statistics
The CDC provides data and statistics on a variety of health related areas.
DataCite
DataCite provides DOI's for research data to help you locate, identify and cite data.
EMBL
EMBL-EBI makes the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics.
Figshare
Allows users to upload any file format to be made visualisable in the browser so that figures, datasets, media, papers, posters, presentations and filesets can be disseminated.
Illinois Experts
Illinois Experts provides access to over 2,000 Illinois researcher profiles through an online, searchable portal, updated weekly from the Scopus abstract and citation database.
Inter-University Consortium for Political and Social Research
The world's largest archive of computerized social science data.
re3data.org
Online directory of research data repositories. Browse by subject or alphabetically, or search by keyword.

Data and Statistics Guides

Data & Statistics for Medicine and Health
Medicine and Health specific data sites.
Finding Social Science Data
This library guide will give you a brief introduction to resources you can use to find social science data for your research. It will guide you in finding resources that list possible data sources, navigating ICPSR, and mining citations from other research articles to help you find data.
Geographic Information Systems (GIS)
This guide will help you get started with understanding what GIS is, the nature of geospatial data used in GIS, and how to get started using GIS for your research.
Social Science, Health, and Education Data and Statistical Sources
This guide will give you a brief introduction to resources you can use to find social science, health and educations statistics and data for your research.
Statistics and Numeric Data
This guide provides links to data resources divided up by subject area.

MetaData

Descriptive Metadata for Datasets DATS Model
from Biocaddie. Alternative link here: https://github.com/biocaddie/WG3-MetadataSpecifications.
United States Heatlh Information Knowledgebase
The United States Health Information Knowledgebase (USHIK) is a metadata registry of healthcare-related data standards funded and directed by the Agency for Healthcare Research and Quality (AHRQ) with management support in partnership with the Centers for Medicare & Medicaid Services.

Engineering & Innovation

Data Science Journals

eBooks

Applied Predictive Modeling

Data Mining

Data Mining

Data Science and Big Data : An Environment of Computational Intelligence

An Introduction to Statistical Learning

Strategies in Biomedical Data Science

Data Science Learning Tools

Data Analysis Tools & Tutorials

Coding & Development Tools

Data Resources from NIH and NLM

Clinical Data Research Networks

General Data Repositories

Data and Statistics Guides

MetaData