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System Information - System Information provides detailed information about your computer’s hardware, software and network in an easy-to-read layout.

Script Editor

Migration Assistant - Simplifies the process of moving your information to another Mac.

Keychain Access - Securely store all your passwords for websites and applications in a keychain.

Grapher - Graph equations and data sets, and visualise the results on your Mac.

Disk Utility - Create, mount, convert, compressed and encrypted disk images, hard drives, DVD.

Digital Color Meter

Console - The Console utility allows you to monitor system logs from a central location.

ColorSync Utility - ColorSync is the built-in colour management system in OS X.

Boot Camp Assistant

Bluetooth File Exchange - Makes it easy to share files between your Mac and Bluetooth-enabled devices.

Audio MIDI Setup - Control settings for all audio going into and out of your Mac.

AirPort Utility - Note: Most recent release available only within OS X 10.11 El Capitan update.

Adobe Flash Player Install Manager

Activity Monitor - Displays information about all the processes running on your Mac.

TeXShop - A straightforward previewer for TeX, a specialized typographic system.

TeX Live Utility - Update, install and manage Tex Live Manager from an intuitive UI.

LaTeXiT - Small utility that allows you to quickly typeset LaTeX equations, without bothering with file creation, preambles, and so on.

Qgis3 - Create, edit, visualise, analyse and publish geospatial information on Mac.

AppCleaner - This program helps you remove unnecessary apps from your Mac.

Aquamacs - A powerful, open-source editor for developers and programmers.

VoiceMemos

Python Launcher

IDLE - — Launch SALE! 50% OFF for a limited time — Idle lets you choose actions to...

Python

GRASS - Grass GIS offers state of the art three-dimensional dynamic spatial analysis and visualization.

Stocks

Cocktail - General purpose utility for OS X that lets you clean, repair and optimize your Mac.

RStudio - RStudio is an integrated development environment (IDE) for R.

R - Language and environment for statistical computing and graphics.

Mactracker - Get immediate access to detailed info about Apple products.

News

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Books - Mac application that lets users manage their in-home books collection by entering in barcodes or by importing from the iCollect Books iPhone/iPod...

KnockKnock - This app helps you find malware threats on your Mac.

Siri - Siri4Mac will bring the basic experience of siri to the mac

TimeMachineEditor - Schedule Time Machine backups with just a few clicks.

Sublime Text - Write and edit various text files using syntax highlighting and a spell checker.

iTerm - iTerm is a full featured terminal emulation program written for OS X using Cocoa

FileZilla - FileZilla (ported from Windows) is a fast and reliable FTP client and server with lots of useful features and an intuitive interface.

Numbers - Plan a wedding. Save for retirement. Track your workouts.

Keynote - Incredible presentations, incredibly easy.

Pages - A document editor for formatted text that provides a Mac alternative to Word.

Zotero - Only research tool that automatically senses content, allowing you to add it to your personal library with a single click.

OpenOffice - OpenOffice.org is both an Open Source product and a project.

OnyX - Multifunctional utility for Mac OS X.