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Ubuntu Software Center, or simply Software Center, is a discontinued high-level graphical front end for the APT/dpkg package management system. It is free software written in Python, PyGTK/PyGObject based on GTK.
The program was created for adding and managing repositories, as well as Ubuntu Personal Package Archives (PPA) and on Ubuntu, the Ubuntu Software Center also allowed users to purchase commercial applications
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Unknown Horizons is a city-building game and real-time strategy game, inspired by the Anno series. It is released under the GNU General Public License (GPLv2) and is therefore free and open source software. Much of the artwork is open content under e
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ViewVC (formerly ViewCVS) is an open-source tool for viewing the contents of CVS and SVN repositories using a web browser. It allows looking at specific revisions of files as well as side-by-side diffs of different revisions. It is written in Python and the view parameters can be modified directly in a URL using a REST style interface
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Virtaal is a computer-assisted translation tool written in the Python programming language. It is free software developed and maintained by Translate. org
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VisTrails is a scientific workflow management system developed at the Scientific Computing and Imaging Institute at the University of Utah that provides support for data exploration and visualization. It is written in Python and employs Qt via PyQt bindings. The system is open source, released under the GPL v2 license
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The Visualization Toolkit (VTK) is an open-source software system for 3D computer graphics, image processing and scientific visualization. VTK is distributed under the OSI-approved BSD 3-clause License.
Functionality
VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python
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Waf is a build automation tool designed to assist in the automatic compilation and installation of computer software. It is written in Python and maintained by Thomas Nagy.
Waf's source code is open source software, released under the terms of the New BSD License, though its accompanying documentation is under the CC-BY-NC-ND license, which forbids both modification and commercial redistribution: this prevents vendors such as the Debian project from including Waf documentation in their distributions
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Wicd, which stands for Wireless Interface Connection Daemon, is an open-source software utility to manage both wireless and wired networks for Linux. The project started in late 2006 with the creation of Connection Manager, which eventually became Wicd. Wicd aims to provide a simple interface to connect to networks with a wide variety of settings
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XPN (X Python Newsreader) is a news client written in Python and based on the GTK+ library.
Features
It offers a good MIME support, scoring system, filtered views, random tag-lines, external editor support, one-key navigation, ROT13, Face and X-Face headers decoding, spoiler char and many more. XPN is free software licensed under the GPL licence
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Xed is a lightweight text editor forked from Pluma and is the default text editor in Linux Mint. Xed is a graphical application which supports editing multiple text files in one window via tabs. It fully supports international text through its use of the Unicode UTF-8 encoding
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The Yellowdog Updater Modified (YUM) is a free and open-source command-line package-management utility for computers running the Linux operating system using the RPM Package Manager. Though YUM has a command-line interface, several other tools provide graphical user interfaces to YUM functionality.
YUM allows for automatic updates and package and dependency management on RPM-based distributions
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In free software, Zeitgeist is a software service which logs the users's activities and events, anywhere from files opened to websites visited and conversations. It makes this information readily available for other applications to use in the form of timelines and statistics. It is able to establish relationships between items based on similarity and usage patterns by applying data association algorithms such as "Winepi" and "Apriori"
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Zope is a family of free and open-source web application servers written in Python, and their associated online community. Zope stands for "Z Object Publishing Environment", and was the first system using the now common object publishing methodology for the Web. Zope has been called a Python killer app, an application that helped put Python in the spotlight
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The Computational Geometry Algorithms Library (CGAL) is an open source software library of computational geometry algorithms. While primarily written in C++, Scilab bindings and bindings generated with SWIG (supporting Python and Java for now) are also available. The software is available under dual licensing scheme
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Cheetah (or CheetahTemplate) is a template engine that uses the Python programming language. It can be used standalone or combined with other tools and frameworks. It is often used for server-side scripting and dynamic web content by generating HTML, but can also be used to generate source code
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Construct is a Python library for the construction and deconstruction of data structures in a declarative fashion. In this context, construction, or building, refers to the process of converting (serializing) a programmatic object into a binary representation. Deconstruction, or parsing, refers to the opposite process of converting (deserializing) binary data into a programmatic object
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Dask is an open-source Python library for parallel computing. Dask scales Python code from multi-core local machines to large distributed clusters in the cloud. Dask provides a familiar user interface by mirroring the APIs of other libraries in the PyData ecosystem including: Pandas, scikit-learn and NumPy
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DVC is a free and open-source, platform-agnostic version system for data, machine learning models, and experiments. It is designed to make ML models shareable, experiments reproducible, and to track versions of models, data, and pipelines. DVC works on top of Git repositories and cloud storage
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Genshi is a template engine for XML-based vocabularies written in
Python. Genshi is used to easily insert generated output into XML-based languages, usually HTML, and reuse elements between documents. Genshi's syntax is based on Kid, but its architecture is different
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IronPython is an implementation of the Python programming language targeting the . NET Framework and Mono. The project is currently maintained by a group of volunteers at GitHub
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Jinja is a web template engine for the Python programming language. It was created by Armin Ronacher and is licensed under a BSD License. Jinja is similar to the Django template engine but provides Python-like expressions while ensuring that the templates are evaluated in a sandbox
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Kid is a simple template engine for XML-based vocabularies written in Python. Kid claims to have many of the best features of XSLT, TAL, and PHP, but "with much of the limitations and complexity stamped out".
Kid initially acted as the View component of the TurboGears framework in the framework's version 1
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Kivy is a free and open source Python framework for developing mobile apps and other multitouch application software with a natural user interface (NUI). It is distributed under the terms of the MIT License, and can run on Android, iOS, Linux, macOS, and Windows.
Kivy is the main framework developed by the Kivy organization, alongside Python for Android, Kivy iOS, and several other libraries meant to be used on all platforms
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The Natural Language Toolkit, or more commonly NLTK, is a suite of libraries and programs for symbolic and statistical natural language processing (NLP) for English written in the Python programming language. It supports classification, tokenization, stemming, tagging, parsing, and semantic reasoning functionalities. It was developed by Steven Bird and Edward Loper in the Department of Computer and Information Science at the University of Pennsylvania
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In computing, serialization (or serialisation) is the process of translating a data structure or object state into a format that can be stored (e. g. files in secondary storage devices, data buffers in primary storage devices) or transmitted (e
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Pygame is a cross-platform set of Python modules designed for writing video games. It includes computer graphics and sound libraries designed to be used with the Python programming language.
History
Pygame was originally written by Pete Shinners to replace PySDL after its development stalled
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PyGTK is a set of Python wrappers for the GTK graphical user interface library. PyGTK is free software and licensed under the LGPL. It is analogous to PyQt/PySide and wxPython, the Python wrappers for Qt and wxWidgets, respectively
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Python Imaging Library is a free and open-source additional library for the Python programming language that adds support for opening, manipulating, and saving many different image file formats. It is available for Windows, Mac OS X and Linux. The latest version of PIL is 1
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Python Robotics (Pyro) is a project designed to create an easy-to-use interface for accessing and controlling a wide variety of real and simulated robots.
History
Pyrobot was funded from 2003 to 2005 by the National Science Foundation as NSF DUE CCLI-EMD Award number 0231363, "Beyond LEGOs: Hardware, Software, and Curriculum for the Next Generation Robot Laboratory". The principal investigators on the NSF grant were Douglas Blank of Bryn Mawr College, Kurt Konolige of SRI International, Deepak Kumar (computer scientist) of Bryn Mawr College, Lisa Meeden of Swarthmore College, and Holly Yanco of University of Massachusetts Lowell
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Python-Ogre is a Python binding for the OGRE 3D engine, designed to provide the functionality and performance of OGRE (written in C++) with the accessibility and ease of use of Python to facilitate the rapid development of 3D games and to make the OGRE engine more accessible to the beginner, who might otherwise be daunted by the technicalities of writing in the native C++. The performance of the engine is decreased in comparison to the original C++ demos, however the original OGRE engine provides such high performance that the performance of Python-Ogre is still more than acceptable for all but the most graphics-intensive games.
Features
Python-Ogre is different from the Ogre3D engine it is based upon as it comes pre-bundled with Python bindings and demos for many other support libraries
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QAL is an open-source development project that aims to create a collection of libraries for mixing, moving, merging, substituting and transforming data; also in some cases, such as MongoDB, schemas.
Description
Sources and destinations include different database backends, file formats like . csv, XML and spreadsheets
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RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information. This library contains parsers/serializers for almost all of the known RDF serializations, such as RDF/XML, Turtle, N-Triples, & JSON-LD, many of which are now supported in their updated form (e. g
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Redland is a set of free software libraries written in C that provide support for the Resource Description Framework (RDF), created by Dave Beckett (a former resident of Redland, Bristol).
The packages that form Redland are:
Redland RDF Application Framework providing the C RDF API
Raptor RDF Parser Toolkit for parsing and serializing RDF syntaxes (RDF/XML, N-Triples, Turtle, RSS tag soup, Atom)
Rasqal RDF Query Library for executing RDF queries with RDQL and SPARQL
Redland Language Bindings for APIs to Redland in C#, Java, Objective-C, Perl, PHP, Python, Ruby and TclRedland is a mature set of libraries, in development since 2000 and closely conformant to the relevant W3C specifications.
See also
Semantic Web
External links
http://librdf
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Requests is an HTTP client library for the Python programming language. Requests is one of the most, if not the most, popular Python libraries that is not included with Python due to its elegant mapping of the HTTP protocol onto Python's object-oriented semantics. Requests's design has inspired and been copied by HTTP client libraries for other programming languages
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RPyC (pronounced are-pie-see), or Remote Python Call, is a Python library for remote procedure calls (RPC), as well as distributed computing. Unlike regular RPC mechanisms, such as ONC RPC, CORBA or Java RMI, RPyC is transparent, symmetric, and requires no special decoration or definition languages. Moreover, it provides programmatic access to any pythonic element, be it functions, classes, instances or modules
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SimPy is a process-based discrete-event simulation framework based on standard Python. It enables users to model active components such as customers, vehicles, or agents as simple Python generator functions. SimPy is released as open source software under the MIT License
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The Sound Object (SndObj) Library is a C++ object-oriented programming library for music and audio development. It is composed of 100+ classes for signal processing, audio, MIDI, and file I/O. The library is available for Linux, Windows, Mac OS X, IRIX, and other Unix-like systems
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SQLAlchemy is an open-source SQL toolkit and object-relational mapper (ORM) for the Python programming language released under the MIT License.
Description
SQLAlchemy's philosophy is that relational databases behave less like object collections as the scale gets larger and performance starts being a concern, while object collections behave less like tables and rows as more abstraction is designed into them. For this reason it has adopted the data mapper pattern (similar to Hibernate for Java) rather than the active record pattern used by a number of other object-relational mappers
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SQLObject is a Python object-relational mapper between a SQL database and Python objects. It is experiencing community popularity, and forms a part of many applications (e. g
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Storm is a Python programming library for object-relational mapping between one or more SQL databases and Python objects. It allows Python developers to formulate complex queries spanning multiple database tables to support dynamic storage and retrieval of object information.
MySQL, PostgreSQL and SQLite database support is built into Storm, and the API allows for support for others
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VPython is the Python programming language plus a 3D graphics module called Visual. VPython allows users to create objects such as spheres and cones in 3D space and displays these objects in a window. This makes it easy to create simple visualizations, allowing programmers to focus more on the computational aspect of their programs
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wxPython is a wrapper for the cross-platform GUI API (often referred to as a "toolkit") wxWidgets (which is written in C++) for the Python programming language. It is one of the alternatives to Tkinter. It is implemented as a Python extension module (native code)
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XDMF (eXtensible Data Model and Format) provides a standard way to access data produced by HPC codes. Data format refers to the raw data to be manipulated, the description of the data is separate from the values themselves. It distinguishes the metadata (Light data) and the values themselves (Heavy data)
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The Blender Game Engine was a free and open-source 3D production suite used for making real-time interactive content. It was previously embedded within Blender, but support for it was dropped in 2019, with the release of Blender 2. 8
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Cocos2d is an open-source game development framework for creating 2D games and other graphical software for iOS, Android, Windows, macOS, Linux, HarmonyOS, OpenHarmony and web platforms. It is written in C++ and provides bindings for various programming languages, including C++, C#, Lua, and JavaScript. The framework offers a wide range of features, including physics, particle systems, skeletal animations, tile maps, and others
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Crystal Space is an unmaintained framework for developing 3D applications written in C++ by Jorrit Tyberghein and others. The first public release was on August 26, 1997. It is typically used as a game engine but the framework is more general and can be used for any kind of 3D visualization
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Delta3d is an open source software gaming/simulation engine API. Delta3d is managed and supported by Caper Holdings LLC. Previously the Modeling, Virtual Environments, and Simulation (MOVES) Institute at the Naval Postgraduate School in Monterey, California managed and supported delta3d
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Panda3D is a game engine that includes graphics, audio, I/O, collision detection, and other abilities relevant to the creation of 3D games. Panda3D is free, open-source software under the revised BSD license.
Panda3D's intended game-development language is Python
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The Spring Engine (also termed SpringRTS and formerly TA Spring), is a game engine for real-time strategy (RTS) video games. The game engine is free and open-source software, subject to the terms of the GNU General Public License v2. 0 or later
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Eve Online (stylised EVE Online) is a space-based, persistent world massively multiplayer online role-playing game (MMORPG) developed and published by CCP Games. Players of Eve Online can participate in a number of in-game professions and activities, including mining, piracy, manufacturing, trading, exploration, and combat (both player versus environment and player versus player). The game contains a total of 7,800 star systems that can be visited by players
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Ni no Kuni II: Revenant Kingdom is an action role-playing game developed by Level-5 and published by Bandai Namco Entertainment. The game is a sequel to Ni no Kuni: Wrath of the White Witch, and was released for PlayStation 4 and Windows on March 23, 2018. The game was later released for the Nintendo Switch on September 17, 2021, and for Xbox One and Xbox Series X/S on March 21, 2023
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Nickelodeon All-Star Brawl 2 is an upcoming crossover fighting game developed by Ludosity and Fair Play Labs, and published by GameMill Entertainment. It is the sequel to Nickelodeon All-Star Brawl (2021) and an entry in the Nickelodeon Super Brawl series. The game is scheduled for release in late 2023 for Nintendo Switch, PlayStation 4, PlayStation 5, Windows, Xbox One, and Xbox Series X/S
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Nine Parchments is a twin stick action role-playing game developed and published by Frozenbyte. The game was released for Nintendo Switch, Windows, and PlayStation 4 in 2017, and for Xbox One in 2018. The game's story revolves around students of the Astral Academy searching for the missing nine parchments
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Ninja Gaiden 3: Razor's Edge is a 2012 action adventure hack and slash game developed by Team Ninja and published by Nintendo. It was released for the Wii U from November 2012 to May 2013, and subsequently released by Tecmo Koei for the PlayStation 3 and Xbox 360 in April 2013. It is an enhanced port of Ninja Gaiden 3 that includes all downloadable content from the original title, as well as additional enhancements made to improve the game
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Ninja Master's: Haō Ninpō Chō, (ニンジャマスターズ ～覇王忍法帖～, Ninja Master's Scrolls of the Supreme Ninja Arts), is a ninja-themed 2D fighting game produced by ADK and originally released in 1996 for the Neo Geo arcade and home platform. Ninja Master's was the sixth and final fighting game produced by ADK, following the four games in the World Heroes series and Aggressors of Dark Kombat. It was later featured in the 2008 compilation ADK Damashii for the PlayStation 2
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No Man's Sky is an action-adventure survival game developed and published by Hello Games. It was released worldwide for the PlayStation 4 and Windows in August 2016, for Xbox One in July 2018, for the PlayStation 5 and Xbox Series X and Series S consoles in November 2020, for Nintendo Switch in October 2022, and for macOS in June 2023. The game is built around five pillars: exploration, survival, combat, trading and base building
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No One Lives Under the Lighthouse is a 2020 horror-adventure game developed by Marevo Collective.
Development
The game was developed by independent game developer Marevo Collective and released on April 21, 2020, as a PC game. Marevo Collective and Torture Star Video released the game on PlayStation 4, PlayStation 5, Nintendo Switch, Xbox One and Xbox Series X and Series S on May 18, 2023
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Johannes Boye Petersen (29 September 1887 – 22 March 1961) was a Danish botanist and phycologist, mainly working on diatoms.
Selected scientific works
Studies on the Biology and Taxonomy of Soil Algae. Dansk Botanisk Arkiv vol
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Kadri Põldmaa (born 28 April 1970 in Tartu) is an Estonian mycologist. Põldmaa is the daughter of mycologist Peeter Põldmaa (1929–1990). She graduated from Tartu Secondary School No
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René Pomerleau, OC (27 April 1904 in Saint-Ferdinand, Quebec – 11 October 1993 in Quebec City) was a mycologist and plant pathologist whose specialty was fungi and lichens. He received a Bachelor of Agricultural Science from Laval University before an MS at the McGill University and later study at the Sorbonne. In 1972, he was awarded an honorary doctorate from Sir George Williams University, which later became Concordia University
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Florian Porcius (August 28 [O. S. August 16] 1816–May 30 [O
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Phytolacca dioica, commonly known as ombú, is a massive evergreen tree in the Pokeweed Family (Phytolaccaceae) native to the Pampas of South America. As its specific epithet suggests, it is dioecious, with male and female flowers on separate plants. The flowers are pollinated by the butterfly Doxocopa laurentia
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Prunus subcoriacea is a species of tree in the family Rosaceae. It is native to South America.
Description
P
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Ruprechtia salicifolia (native name viraró) is a timber tree native to South America. Its wood withstands decay and is good for making springboards and other articles.
Description
A thicket-forming shrub or dioecious tree native to South America, it is a perennial phanerogamous or seed producing plant in the Polygonaceae family
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Sambucus peruviana is a species of tree in the family Adoxaceae. It is native to Central America and South America.
Description
Trees up to 8 m, irregular trunk
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Gregory James Hannon (born 1964) is a professor of molecular cancer biology and director of the Cancer Research UK Cambridge Institute at the University of Cambridge. He is a Fellow of Trinity College, Cambridge while also serving as a director of cancer genomics at the New York Genome Center and an adjunct professor at Cold Spring Harbor Laboratory.
Career and research
Hannon is known for his contributions to small RNA biology, cancer biology, and mammalian genomics
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Antibody mimetics are organic compounds that, like antibodies, can specifically bind antigens, but that are not structurally related to antibodies. They are usually artificial peptides or proteins with a molar mass of about 3 to 20 kDa. (Antibodies are ~150 kDa
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Affilins are artificial proteins designed to selectively bind antigens. Affilin proteins are structurally derived from human ubiquitin (historically also from gamma-B crystallin). Affilin proteins are constructed by modification of surface-exposed amino acids of these proteins and isolated by display techniques such as phage display and screening
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Affitins (commercial name Nanofitins) are artificial proteins with the ability to selectively bind antigens. They are structurally derived from the DNA binding protein Sac7d, found in Sulfolobus acidocaldarius, a microorganism belonging to the archaeal domain. By randomizing the amino acids on the binding surface of Sac7d and subjecting the resulting protein library to rounds of ribosome display, the affinity can be directed towards various targets, such as peptides, proteins, viruses, and bacteria
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Alphabodies, also known as Cell-Penetrating Alphabodies or CPAB for short, are small 10 kDa proteins engineered to bind to a variety of antigens. Despite their name, they are not structurally similar to antibodies, which makes them a type of antibody mimetic. Alphabodies are different from many other antibody mimetics in their ability to reach and bind to intracellular protein targets
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Anticalin proteins are artificial proteins that are able to bind to antigens, either to proteins or to small molecules. They are not structurally related to antibodies, which makes them a type of antibody mimetic. Instead, they are derived from human lipocalins which are a family of naturally binding proteins
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Ecallantide (trade name Kalbitor) is a drug used for the treatment of hereditary angioedema (HAE) and in the prevention of blood loss in cardiothoracic surgery. It is an inhibitor of the protein kallikrein and a 60-amino acid polypeptide which was developed from a Kunitz domain through phage display to mimic antibodies inhibiting kallikrein.
Medical uses
Angioedema
On November 27, 2009, ecallantide was approved by the FDA for the treatment of acute attacks of hereditary angioedema for persons over 16 years of age
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Kunitz domains are the active domains of proteins that inhibit the function of protein degrading enzymes or, more specifically, domains of Kunitz-type are protease inhibitors. They are relatively small with a length of about 50 to 60 amino acids and a molecular weight of 6 kDa. Examples of Kunitz-type protease inhibitors are aprotinin (bovine pancreatic trypsin inhibitor, BPTI), Alzheimer's amyloid precursor protein (APP), and tissue factor pathway inhibitor (TFPI)
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Kunitz soybean trypsin inhibitor is a type of protein contained in legume seeds which functions as a protease inhibitor. Kunitz-type Soybean Trypsin Inhibitors are usually specific for either trypsin or chymotrypsin. They are thought to protect seeds against consumption by animal predators
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Pegdinetanib (USAN; planned trade name Angiocept) is an investigational anti-cancer drug that acts as a selective antagonist of vascular endothelial growth factor receptor 2 (VEGFR-2), hindering vascularization of tumors. It is a genetically engineered peptide derivative based on the monobody technology, and is being developed by Adnexus. The drug has entered Phase II clinical trials investigating the treatment of glioblastoma in October 2007
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Molecular biophysics is a rapidly evolving interdisciplinary area of research that combines concepts in physics, chemistry, engineering, mathematics and biology. It seeks to understand biomolecular systems and explain biological function in terms of molecular structure, structural organization, and dynamic behaviour at various levels of complexity (from single molecules to supramolecular structures, viruses and small living systems). This discipline covers topics such as the measurement of molecular forces, molecular associations, allosteric interactions, Brownian motion, and cable theory
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Affinity electrophoresis is a general name for many analytical methods used in biochemistry and biotechnology. Both qualitative and quantitative information may be obtained through affinity electrophoresis. Cross electrophoresis, the first affinity electrophoresis method, was created by Nakamura et al
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Agarose gel electrophoresis is a method of gel electrophoresis used in biochemistry, molecular biology, genetics, and clinical chemistry to separate a mixed population of macromolecules such as DNA or proteins in a matrix of agarose, one of the two main components of agar. The proteins may be separated by charge and/or size (isoelectric focusing agarose electrophoresis is essentially size independent), and the DNA and RNA fragments by length. Biomolecules are separated by applying an electric field to move the charged molecules through an agarose matrix, and the biomolecules are separated by size in the agarose gel matrix
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Capillary electrochromatography (CEC) is a chromatographic technique in which the mobile phase is driven through the chromatographic bed by electroosmosis. Capillary electrochromatography is a combination of two analytical techniques, high-performance liquid chromatography and capillary electrophoresis. Capillary electrophoresis aims to separate analytes on the basis of their mass-to-charge ratio by passing a high voltage across ends of a capillary tube, which is filled with the analyte
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https://huggingface.co/datasets/fmars/wiki_stem
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Capillary electrophoresis (CE) is a family of electrokinetic separation methods performed in submillimeter diameter capillaries and in micro- and nanofluidic channels. Very often, CE refers to capillary zone electrophoresis (CZE), but other electrophoretic techniques including capillary gel electrophoresis (CGE), capillary isoelectric focusing (CIEF), capillary isotachophoresis and micellar electrokinetic chromatography (MEKC) belong also to this class of methods. In CE methods, analytes migrate through electrolyte solutions under the influence of an electric field
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https://huggingface.co/datasets/fmars/wiki_stem
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The single cell gel electrophoresis assay (SCGE, also known as comet assay) is an uncomplicated and sensitive technique for the detection of DNA damage at the level of the individual eukaryotic cell. It was first developed by Östling & Johansson in 1984 and later modified by Singh et al. in 1988
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https://huggingface.co/datasets/fmars/wiki_stem
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Dielectrophoresis (DEP) is a phenomenon in which a force is exerted on a dielectric particle when it is subjected to a non-uniform electric field. This force does not require the particle to be charged. All particles exhibit dielectrophoretic activity in the presence of electric fields
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https://huggingface.co/datasets/fmars/wiki_stem
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Difference gel electrophoresis (DIGE) is a form of gel electrophoresis where up to three different protein samples can be labeled with size-matched, charge-matched spectrally resolvable fluorescent dyes (for example Cy3, Cy5, Cy2) prior to two dimensional gel electrophoresis.
Procedure
The three samples are mixed and loaded onto IEF (isoelectric focusing chromatography) for first dimension and the strip is transferred to a SDS PAGE. After the gel electrophoresis, the gel is scanned with the excitation wavelength of each dye one after the other, so each sample can be seen separately (if we scan the gel at the excitation wavelength of the Cy3 dye, we will see in the gel only the sample that was labeled with that dye)
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https://huggingface.co/datasets/fmars/wiki_stem
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Discontinuous electrophoresis (colloquially disc electrophoresis) is a type of polyacrylamide gel electrophoresis. It was developed by Ornstein and Davis. This method produces high resolution and good band definition
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https://huggingface.co/datasets/fmars/wiki_stem
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DNA laddering is a feature that can be observed when DNA fragments, resulting from Apoptosis DNA fragmentation are visualized after separation by gel electrophoresis the first described in 1980 by Andrew Wyllie at the University Edinburgh medical school DNA fragments can also be delected in cells that underwent necrosis, when theses DNA fragments after separation are subjected to gel electrophoresis which in the results in a characteristic ladder pattern,
DNA degradation
DNA laddering is a distinctive feature of DNA degraded by caspase-activated DNase (CAD), which is a key event during apoptosis. CAD cleaves genomic DNA at internucleosomal linker regions, resulting in DNA fragments that are multiples of 180–185 base-pairs in length. Separation of the fragments by agarose gel electrophoresis and subsequent visualization, for example by ethidium bromide staining, results in a characteristic "ladder" pattern
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https://huggingface.co/datasets/fmars/wiki_stem
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Electrical mobility is the ability of charged particles (such as electrons or protons) to move through a medium in response to an electric field that is pulling them. The separation of ions according to their mobility in gas phase is called ion mobility spectrometry, in liquid phase it is called electrophoresis.
Theory
When a charged particle in a gas or liquid is acted upon by a uniform electric field, it will be accelerated until it reaches a constant drift velocity according to the formula
where
v
d
{\displaystyle v_{\text{d}}}
is the drift velocity (SI units: m/s),
E
{\displaystyle E}
is the magnitude of the applied electric field (V/m),
μ
{\displaystyle \mu }
is the mobility (m2/(V·s))
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https://huggingface.co/datasets/fmars/wiki_stem
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Electroblotting is a method in molecular biology/biochemistry/immunogenetics to transfer proteins or nucleic acids onto a membrane by using PVDF or nitrocellulose, after gel electrophoresis. The protein or nucleic acid can then be further analyzed using probes such as specific antibodies, ligands like lectins, or stains. This method can be used with all polyacrylamide and agarose gels
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https://huggingface.co/datasets/fmars/wiki_stem
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Electrochemical skin conductance (ESC) is an objective, non-invasive and quantitative electrophysiological measure. It is based on reverse iontophoresis and (multiple) steady chronoamperometry (more specifically chronovoltametry).
ESC is intended to provide insight into and assess sudomotor (or sweat gland) function and small fiber peripheral neuropathy
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https://huggingface.co/datasets/fmars/wiki_stem
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Electrochromatography is a chemical separation technique in analytical chemistry, biochemistry and molecular biology used to resolve and separate mostly large biomolecules such as proteins. It is a combination of size exclusion chromatography (gel filtration chromatography) and gel electrophoresis. These separation mechanisms operate essentially in superposition along the length of a gel filtration column to which an axial electric field gradient has been added
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https://huggingface.co/datasets/fmars/wiki_stem
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An electrophoretic color marker is a chemical used to monitor the progress of agarose gel electrophoresis and polyacrylamide gel electrophoresis (PAGE) since DNA, RNA, and most proteins are colourless. The color markers are made up of a mixture of dyes that migrate through the gel matrix alongside the sample of interest. They are typically designed to have different mobilities from the sample components and to generate colored bands that can be used to assess the migration and separation of sample components
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https://huggingface.co/datasets/fmars/wiki_stem
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An electrophoretic mobility shift assay (EMSA) or mobility shift electrophoresis, also referred as a gel shift assay, gel mobility shift assay, band shift assay, or gel retardation assay, is a common affinity electrophoresis technique used to study protein–DNA or protein–RNA interactions. This procedure can determine if a protein or mixture of proteins is capable of binding to a given DNA or RNA sequence, and can sometimes indicate if more than one protein molecule is involved in the binding complex. Gel shift assays are often performed in vitro concurrently with DNase footprinting, primer extension, and promoter-probe experiments when studying transcription initiation, DNA gang replication, DNA repair or RNA processing and maturation, as well as pre-mRNA splicing
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https://huggingface.co/datasets/fmars/wiki_stem
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Complete-linkage clustering is one of several methods of agglomerative hierarchical clustering. At the beginning of the process, each element is in a cluster of its own. The clusters are then sequentially combined into larger clusters until all elements end up being in the same cluster
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https://huggingface.co/datasets/fmars/wiki_stem
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In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids (DNA and RNA) or proteins across species (orthologous sequences), or within a genome (paralogous sequences), or between donor and receptor taxa (xenologous sequences). Conservation indicates that a sequence has been maintained by natural selection.
A highly conserved sequence is one that has remained relatively unchanged far back up the phylogenetic tree, and hence far back in geological time
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https://huggingface.co/datasets/fmars/wiki_stem
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The method of covarions, or concomitantly variable codons, is a technique in computational phylogenetics that allows the hypothesized rate of molecular evolution at individual codons in a set of nucleotide sequences to vary in an autocorrelated manner. Under the covarion model, the rates of evolution on different branches of a hypothesized phylogenetic tree vary in an autocorrelated way, and the rates of evolution at different codon sites in an aligned set of DNA or RNA sequences vary in a separate but autocorrelated manner. This provides additional and more realistic constraints on evolutionary rates versus the simpler technique of allowing the rate of evolution on each branch to be selected randomly from a suitable probability distribution such as the gamma distribution
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https://huggingface.co/datasets/fmars/wiki_stem
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Distance matrices are used in phylogeny as
non-parametric distance methods and were originally applied to phenetic data using a matrix of pairwise distances. These distances are then reconciled to produce a tree (a phylogram, with informative branch lengths). The distance matrix can come from a number of different sources, including measured distance (for example from immunological studies) or morphometric analysis, various pairwise distance formulae (such as euclidean distance) applied to discrete morphological characters, or genetic distance from sequence, restriction fragment, or allozyme data
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https://huggingface.co/datasets/fmars/wiki_stem
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A Gap penalty is a method of scoring alignments of two or more sequences. When aligning sequences, introducing gaps in the sequences can allow an alignment algorithm to match more terms than a gap-less alignment can. However, minimizing gaps in an alignment is important to create a useful alignment
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https://huggingface.co/datasets/fmars/wiki_stem
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In phylogenetics, informative site is a term used when maximum parsimony is the optimality criterion for construction of a phylogenetic tree. It refers to a characteristic for which the number of character-state evolutionary changes of at this site depends on the topology of the tree. The charactetistics can take on multiple types of data, including morphological (such as the presence of wings, tentacles, etc
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https://huggingface.co/datasets/fmars/wiki_stem
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Least squares inference in phylogeny generates a
phylogenetic tree based on an
observed matrix of pairwise genetic distances and
optionally a weight
matrix. The goal is to find a tree which satisfies the distance constraints as
best as possible.
Ordinary and weighted least squares
The discrepancy between the observed pairwise distances
D
i
j
{\displaystyle D_{ij}}
and the distances
T
i
j
{\displaystyle T_{ij}}
over a phylogenetic tree (i
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https://huggingface.co/datasets/fmars/wiki_stem
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In phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes (or minimizes the cost of differentially weighted character-state changes). Under the maximum-parsimony criterion, the optimal tree will minimize the amount of homoplasy (i. e
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https://huggingface.co/datasets/fmars/wiki_stem
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Minimum evolution is a distance method employed in phylogenetics modeling. It shares with maximum parsimony the aspect of searching for the phylogeny that has the shortest total sum of branch lengths. The theoretical foundations of the minimum evolution (ME) criterion lay in the seminal works of both Kidd and Sgaramella-Zonta and Rzhetsky and Nei
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https://huggingface.co/datasets/fmars/wiki_stem
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