This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"The laboratory and computational tools available to microbiome researchers have greatly improved in recent years, especially in assembling genomes from complex communities. Most of the research to date has focused on macrodiversity, which is classical ecology metrics like population abundance, α-diversity, and β-diversity. But microdiversity — population genetics metrics like single nucleotide polymorphisms (SNPs) and selective pressures — is important to consider. There are several technical and accessibility issues that hinder widespread analysis of microdiversity in metagenomic datasets, but the recently developed open-access software tool MetaPop is designed to close this gap. MetaPop provides a user-friendly interface to analyze both the macro- and microdiversity of microbial and viral community metagenomes. For small datasets, MetaPop can be run on a laptop, making it a practical choice for non-bioinformaticians or labs without access to high-powered computing..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Learn how Sally Ride inspired engineer Shirley Kozler who now works for Wing.

Today, computer-based simulations are becoming increasingly popular, especially when daylighting and energy conservation are amongst the key goals for a project. This two-week workshop will expose participants to the current daylighting simulation models and beyond, by introducing realistic and dynamic assessment methods through hands-on exercises and application to a design project. Open to students and practitioners.
This course is offered during the Independent Activities Period (IAP), which is a special 4-week term at MIT that runs from the first week of January until the end of the month.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Reproducibility is extremely important in science. But no matter how much effort is put into standardizing protocols, small differences seem inevitable in the way experiments are performed among laboratories. These small differences can add up to discrepancies that complicate data interpretation. One field where this issue looms large is neuroscience – particularly in experiments involving histological sections of the mouse brain. Such studies require correct identification of specific brain regions for accurate interpretation of results. But the mouse brain is small and complex. Brain atlases can be invaluable in mapping, but applying this information in laboratory experiments is difficult. A new automated system aims to solve this problem by taking the guesswork – and potential observer error and bias – out of the equation. Much like a GPS system in a car, the program – called NeuroInfo – helps researchers navigate through the microscopic anatomy of a brain section..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Uncovering the links between microbiome profiles and host conditions is critical to understanding the roles microbes play in human health. However, analysis of microbiome profiles with traditional testing frameworks is made difficult by the high-dimensionality and sparsity of the data. Often this is addressed by incorporating information from closely related microbes. This phylogenetic information is added under the assumption that operational taxonomic units (OTUs) from related taxa will tend to behave similarly, but the complexity of microbe interactions can make this assumption invalid. The recently developed tool, Phylogeny-guided microbiome OTU-Specific association Test (POST), addresses this issue. POST determines how much, if any, information to borrow from neighboring OTUs based on phylogenetic distance and outcome-OTU association. This tool is a local collapsing test built under the kernel machine framework to accommodate complex OTU effects..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Training Modules developed for Ocean Sciences Meeting 2020 and recorded for sharing at European Geosciences Union 2020 General Assembly.

Digital technologies old and new are not objects that can be packed inside a box. They are a seamless, indivisible combination of people, organizations, policies, economies, histories, cultures, knowledge, and material things that are continuously shaped and reshaped. Every one of us innovates-in-use our everyday technologies; we just do not always know it. We are shaped by the networked information tools in our midst, and we shape them and thereby shape others. While many of the chapters in this book can be approached as standalone explorations, as many around the world have done, its full potential comes when collaboratively taken as a journey through twelve sessions. Each session in this second, revised edition includes two thematically linked chapters, one more socially oriented and one more technically oriented. Sessions are brought together into three larger generative themes that are built from three decades of participatory design in and with community, and from the teaching of these concepts and practices in courses and workshops. Approached within a community of practice, learning outcomes include discovering ways to advance power, both power within and power with others; advancing our technical skills, but also and even more, our progressive community engagement skills, our critical sociotechnical skills, and our cognitive, information, and social-emotional skills; and progressing our culturally competent collective leadership through social justice storytelling within a framing of reciprocity. In so doing, this textbook seeks to address the call placed by the Rev. Dr. Martin Luther King, Jr. – to rapidly shift from a ‘thing-oriented’ society to a ‘person-oriented’ society.

In this culminating activity of the unit, students bring together everything they've learned in order to write the code to solve the Grand Challenge. The code solution takes two images captured by robots and combines them to create an image that can be focused at different distances, similar to the way that humans can focus either near or far. They write in a derivative of C++ called QT; all code is listed in this activity.

Sample Wrench is an extensive digital audio analysis and editing tool that runs under Windows. Formerly a commercial product for many years, I recently placed this as non-commercial redistributable freeware. It is useful for coursework in electronics, audio, acoustics, music production and the like. Opens and saves .wav and other popular sound files. Waveforms can be viewed in the time domain like a digital oscilloscope and also via 2D and pseudo 3D spectral displays. Features a wide array of editing tools including EQ, filtering, pitch shifting, time compression, spectral warping, etc. Also offers a macro language which allows batch processing and the creation of custom functions.

More information about it can be found at http://www.dissidents.com/audio.htm

This unit covers common security concerns and safeguards, including firewalls, encryption, virus protection software and patterns, and programming for security. Additional topics include security of wireless networks, and concerns, mitigations, and regulations related to healthcare applications.

This course presents software engineering concepts and principles in parallel with the software development life cycle. Topics addressed include the Software Development Life Cycle (SDLC), software modeling using Unified Modeling Language (UML), major phases of SDLC (Software Requirements and Analysis, Software Design, and Software Testing), and project management. Upon successful completion of this course, the student will be able to: demonstrate mastery of software engineering knowledge and skills, and professional issues necessary to practice software engineering; discuss principles of software engineering; describe software development life cycle models; learn principles of software modeling through UML as a modeling language; identify major activities and key deliverables in a software development life cycle during software requirements and analysis, software design, and software testing; apply the object-oriented methodology in software engineering to create UML artifacts for software analysis and requirements, software design, and software testing; apply project management concepts in a software engineering environment to manage project, people, and product; participate as an individual and as part of a team to deliver quality software systems. This free course may be completed online at any time. (Computer Science 302)

This course on software engineering covers design and implementation of medium-scale software systems, using web applications as a platform. In the course, students learn the fundamentals of structuring a web application and writing modular code, with an emphasis on conceptual design to achieve clarity, simplicity, and modularity. Topics also include functional programming, relational databases, and security.

statcheck is a program that checks for errors in statistical reporting in APA-formatted documents. It was originally written in the R programming language. statcheck/web is a web-based implementation of statcheck. Using statcheck/web, you can check any PDF for statistical errors without installing the R programming language on your computer.

From the website: "Statistics With Technology, Second Edition, is an introductory statistics textbook. It uses the TI-83/84 calculator and R, an open source statistical software, for all calculations. Other technology can also be used besides the TI-83/84 calculator and the software R, but these are the ones that are presented in the text. This book presents probability and statistics from a more conceptual approach, and focuses less on computation. Analysis and interpretation of data is more important than how to compute basic statistical values.
License: Creative Commons Attribution Sharealike. This license is considered to be some to be the most open license. It allows reuse, remixing, and distribution (including commercial), but requires any remixes use the same license as the original. This limits where the content can be remixed into, but on the other hand ensures that no-one can remix the content then put the remix under a more restrictive license.
Formats:
DOC. A DOC file can be opened using Microsoft Word or OpenOffice.org. It is an editable format
PDF. A Portable Document Format (PDF) file is can be opened using the free Acrobat Reader. It is not an editable format.
Openness Rating (0-4): 3.5"

Students observe natural selection in action and investigate the underlying mechanism, including random mutation and differential fitness based on environmental characteristics. They do this through use of the free AVIDA-ED digital evolution software application.

Students gain experience using the software/systems (engineering) design process, specifically focusing on the testing phase. This problem-based learning activity uses the design process to solve open-ended challenges. In addition to learning about test cases for testing software, students utilize the design process as a vehicle to work through a problem and arrive at a solution.

JUnit is a testing method that is included with NetBeans (Java) installs or can be downloaded from the web and included in the Java build. In this activity, students design tests for a provided Java class before the class methods are constructed using a process called test-driven development. To create a design, the software/system design process, which is a specific case of the engineering design process, is followed. After students create a design, it is implemented and tested and if necessary, the design undergoes editing to make sure it functions by testing the Java class correctly. To conclude the activity, students write the methods in the Java class using their tests to debug the program.

Students learn basic concepts of robotic logic and programming by working with Boe-Bot robots—a simple programmable robotic platform designed to illustrate basic robotic concepts. Under the guidance of the instructor and a provided lab manual, student groups build simple circuits and write codes to make their robots perform a variety of tasks, including obstacle and light detection, line following and other motion routines. Eight sub-activities focus on different sensors, including physical sensors, phototransistors and infrared headlights. Students test their newly acquired skills in the final activity, in which they program their robots to navigate an obstacle course.

As part of our NSF-funded passion-driven statistics project, we have just started to share more widely our “translation code” aimed at supporting folks in learning code-based software and in moving more easily between them.  The pdf includes all of the basic syntax for managing, displaying and analyzing data, translated across SAS, R, Python, Stata and SPSS.

Students focus on the testing phase of the design process by considering how they have tested computer programs in the past and learning about a new method called JUnit to test programs in the future. JUnit is a testing method that is included with NetBeans (Java) installs or can be downloaded from the web and included in the Java build. Students design tests using JUnit and implement those tests.