Digital organism

A digital organism is a self-replicating computer program that mutates and evolves. Digital organisms are used as a tool to study the dynamics of Darwinian evolution, and to test or verify specific hypotheses or mathematical models of evolution. The study of digital organisms is closely related to the area of artificial life. == History == Digital organisms can be traced back to the game Darwin, developed in 1961 at Bell Labs, in which computer programs had to compete with each other by trying to stop others from executing . A similar implementation that followed this was the game Core War. In Core War, it turned out that one of the winning strategies was to replicate as fast as possible, which deprived the opponent of all computational resources. Programs in the Core War game were also able to mutate themselves and each other by overwriting instructions in the simulated "memory" in which the game took place. This allowed competing programs to embed damaging instructions in each other that caused errors (terminating the process that read it), "enslaved processes" (making an enemy program work for you), or even change strategies mid-game and heal themselves. Steen Rasmussen at Los Alamos National Laboratory took the idea from Core War one step further in his core world system by introducing a genetic algorithm that automatically wrote programs. However, Rasmussen did not observe the evolution of complex and stable programs. It turned out that the programming language in which core world programs were written was very brittle, and more often than not mutations would completely destroy the functionality of a program. The first to solve the issue of program brittleness was Thomas S. Ray with his Tierra system, which was similar to core world. Ray made some key changes to the programming language such that mutations were much less likely to destroy a program. With these modifications, he observed for the first time computer programs that did indeed evolve in a meaningful and complex way. Later, Chris Adami, Titus Brown, and Charles Ofria started developing their Avida system, which was inspired by Tierra but again had some crucial differences. In Tierra, all programs lived in the same address space and could potentially execute or otherwise interfere with each other's code. In Avida, on the other hand, each program lives in its own address space. Because of this modification, experiments with Avida became much cleaner and easier to interpret than those with Tierra. With Avida, digital organism research has begun to be accepted as a valid contribution to evolutionary biology by a growing number of evolutionary biologists. Evolutionary biologist Richard Lenski of Michigan State University has used Avida extensively in his work. Lenski, Adami, and their colleagues have published in journals such as Nature and the Proceedings of the National Academy of Sciences (USA). In 1996, Andy Pargellis created a Tierra-like system called Amoeba that evolved self-replication from a randomly seeded initial condition. More recently REvoSim - a software package based around binary digital organisms - has allowed evolutionary simulations of large populations that can be run for geological timescales.

Arabic Ontology

Arabic Ontology is a website offering linguistic ontology services for the Arabic language which can be used like the online site WordNet. Users can use Arabic Ontology to classify or clarify the concepts and meanings of Arabic terms. == Ontology Structure == The ontology structure (i.e., data model) is similar to WordNet's structure. Each concept in the database is given a unique concept identifier (URI), informally described by a gloss, and lexicalized by one or more synonymous lemma terms. Each term-concept pair is called a sense, and is given a SenseID. A set of senses is called synset. Concepts and senses are described by further attributes such as era and area — to specify example usage and ontological analysis. Semantic relations are defined between concepts. Some important entities are included in the ontology, such as individual countries and bodies of water. These individuals are given separate IndividualIDs and linked with their concepts through the InstanceOf relation. == Mappings to other resources == Concepts in the Arabic Ontology are mapped to synsets in WordNet, as well as to BFO and DOLCE. Terms used in the Arabic Ontology are mapped to lemmas in the LDC's SAMA database. == Applications == Arabic Ontology can be used in many application domains, such as: Information retrieval, to enrich queries (e.g., in search engines) and improve the quality of the results, i.e. meaningful search rather than string-matching search; Machine translation and word-sense disambiguation, by finding the exact mapping of concepts across languages, especially that the Arabic ontology is also mapped to the WordNet; Data Integration and interoperability in which the Arabic ontology can be used as a semantic reference to link databases and information systems; Semantic Web and Web 3.0, by using the Arabic ontology as a semantic reference to disambiguate the meanings used in websites; among many other applications. == URLs Design == The URLs in the Arabic Ontology are designed according to the W3C's Best Practices for Publishing Linked Data, as described in the following URL schemes. This allows one to also explore the whole database like exploring a graph: Ontology Concept: Each concept in the Arabic Ontology has a ConceptID and can be accessed using: https://{domain}/concept/{ConceptID | Term}. In case of a term, the set of concepts that this term lexicalizes are all retrieved. In case of a ConceptID, the concept and its direct subtypes are retrieved, e.g. https://ontology.birzeit.edu/concept/293198 Semantic relations: Relationships between concepts can be accessed using these schemes: (i) the URL: https:// {domain}/concept/{RelationName}/{ConceptID} allows retrieval of relationships among ontology concepts. (ii) the URL: https://{domain}/lexicalconcept/{RelationName}/{lexicalConceptID} allows retrieval of relations between lexical concepts. For example, https://ontology.birzeit.edu/concept/instances/293121 retrieves the instances of the concept 293121. The relations that are currently used in our database are: {subtypes, type, instances, parts, related, similar, equivalent}.

Biopython

Biopython is an open-source collection of non-commercial Python modules for computational biology and bioinformatics. It makes robust and well-tested code easily accessible to researchers. Python is an object-oriented programming language and is a suitable choice for automation of common tasks. The availability of reusable libraries saves development time and lets researchers focus on addressing scientific questions. Biopython is constantly updated and maintained by a large team of volunteers across the globe. Biopython contains parsers for diverse bioinformatic sequence, alignment, and structure formats. Sequence formats include FASTA, FASTQ, GenBank, and EMBL. Alignment formats include Clustal, BLAST, PHYLIP, and NEXUS. Structural formats include the PDB, which contains the 3D atomic coordinates of the macromolecules. It has provisions to access information from biological databases like NCBI, Expasy, PBD, and BioSQL. This can be used in scripts or incorporated into their software. Biopython contains a standard sequence class, sequence alignment, and motif analysis tools. It also has clustering algorithms, a module for structural biology, and a module for phylogenetics analysis. == History == The development of Biopython began in 1999, and it was first released in July 2000. First "semi-complete" and "semi-stable" release was done in March 2001 and December 2002 respectively. It was developed during a similar time frame and with analogous goals to other projects that added bioinformatics capabilities to their respective programming languages, including BioPerl, BioRuby and BioJava. Early developers on the project included Jeff Chang, Andrew Dalke and Brad Chapman, though over 100 people have made contributions to date. In 2007, a similar Python project, namely PyCogent, was established. The initial scope of Biopython involved accessing, indexing and processing biological sequence files. The retrieved data from common biological databases will then be parsed into a python data structure. While this is still a major focus, over the following years added modules have extended its functionality to cover additional areas of biology. The key challenge in the design of parsers for bioinformatics file formats is the frequency at which the data formats change. This is due to inadequate curation of the structure of the data, and changes in the database contents. This problem is overcome by the application of a standard event-oriented parser design (see Key features and examples). As of version 1.77, Biopython no longer supports Python 2. The current stable release of Biopython version 1.85 was released on 15 January 2025. It only supports Python 3 and the recent releases of Biopython require NumPy (and not Numeric). == Design == Wherever possible, Biopython follows the conventions used by the Python programming language to make it easier for users familiar with Python. For example, Seq and SeqRecord objects can be manipulated via slicing, in a manner similar to Python's strings and lists. It is also designed to be functionally similar to other Bio projects, such as BioPerl. It is organized into modular sub-packages, e.g., Bio.Seq, Bio.Align, Bio.PDB, Bio.Entrez each of them useful in a different bioinformatics domain. It used principles, like encapsulation and polymorphism, notably in classes Seq, SeqRecord, and Bio.PDB.Structure. It can also interoperate with other Python tools (Pandas, Matplotlib and SciPy). Biopython can read and write most common file formats for each of its functional areas, and its license is permissive and compatible with most other software licenses, which allows Biopython to be used in a variety of software projects. == Requirements == Biopython is currently supported and tested with the following Python implementations: Python 3 or PyPy3 NumPy == Key features and examples == === Input and output === Biopython can read and write to a number of common formats. When reading files, descriptive information in the file is used to populate the members of Biopython classes, such as SeqRecord. This allows records of one file format to be converted into others. Very large sequence files can exceed a computer's memory resources, so Biopython provides various options for accessing records in large files. They can be loaded entirely into memory in Python data structures, such as lists or dictionaries, providing fast access at the cost of memory usage. Alternatively, the files can be read from disk as needed, with slower performance but lower memory requirements. === Sequences === A core concept in Biopython is the biological sequence, and this is represented by the Seq class. A Biopython Seq object is similar to a Python string in many respects: it supports the Python slice notation, can be concatenated with other sequences and is immutable. This object includes both general string-like and biological sequence-specific methods. It is best to store information about the biological type (DNA, RNA, protein) separately from the sequence, rather than using an explicit alphabet argument. === Sequence annotation === The SeqRecord class describes sequences, along with information such as name, description and features in the form of SeqFeature objects. Each SeqFeature object specifies the type of the feature and its location. Feature types can be ‘gene’, ‘CDS’ (coding sequence), ‘repeat_region’, ‘mobile_element’ or others, and the position of features in the sequence can be exact or approximate. === Accessing online databases === Through the Bio.Entrez module, users of Biopython can download biological data from NCBI databases. Each of the functions provided by the Entrez search engine is available through functions in this module, including searching for and downloading records. === Phylogeny === The Bio.Phylo module provides tools for working with and visualising phylogenetic trees. A variety of file formats are supported for reading and writing, including Newick, NEXUS and phyloXML. Common tree manipulations and traversals are supported via the Tree and Clade objects. Examples include converting and collating tree files, extracting subsets from a tree, changing a tree's root, and analysing branch features such as length or score. Rooted trees can be drawn in ASCII or using matplotlib (see Figure 1), and the Graphviz library can be used to create unrooted layouts (see Figure 2). === Genome diagrams === The GenomeDiagram module provides methods of visualising sequences within Biopython. Sequences can be drawn in a linear or circular form (see Figure 3), and many output formats are supported, including PDF and PNG. Diagrams are created by making tracks and then adding sequence features to those tracks. By looping over a sequence's features and using their attributes to decide if and how they are added to the diagram's tracks, one can exercise much control over the appearance of the final diagram. Cross-links can be drawn between different tracks, allowing one to compare multiple sequences in a single diagram. === Macromolecular structure === The Bio.PDB module can load molecular structures from PDB and mmCIF files, and was added to Biopython in 2003. The Structure object is central to this module, and it organises macromolecular structure in a hierarchical fashion: Structure objects contain Model objects which contain Chain objects which contain Residue objects which contain Atom objects. Disordered residues and atoms get their own classes, DisorderedResidue and DisorderedAtom, that describe their uncertain positions. Using Bio.PDB, one can navigate through individual components of a macromolecular structure file, such as examining each atom in a protein. Common analyses can be carried out, such as measuring distances or angles, comparing residues and calculating residue depth. === Population genetics === The Bio.PopGen module adds support to Biopython for Genepop, a software package for statistical analysis of population genetics. This allows for analyses of Hardy–Weinberg equilibrium, linkage disequilibrium and other features of a population's allele frequencies. This module can also carry out population genetic simulations using coalescent theory with the fastsimcoal2 program. === Wrappers for command line tools === Biopython previously included command-line wrappers for tools such as BLAST, Clustal, EMBOSS, and SAMtools. This option allowed users to run external tool commands from within the code using specialized Biopython classes. However, Bio.Application modules and their wrappers have deprecated and will be removed in future Biopython releases. The main reason for this is the high maintenance burden of updating them with the evolving external tools. The recommended approach is to directly construct and execute command-line tool commands using Python’s built-in subprocess module. This method provides flexibility and removes the dependency on the Biopython wrappers. subprocess is a native Python module useful for running ext

Azure Data Lake

Azure Data Lake is a scalable data storage and analytics service. The service is hosted in Azure, Microsoft's public cloud. == History == Azure Data Lake service was released on November 16, 2016. It is based on COSMOS, which is used to store and process data for applications such as Azure, AdCenter, Bing, MSN, Skype and Windows Live. COSMOS features a SQL-like query engine called SCOPE upon which U-SQL was built. == Storage == Data Lake Storage is a cloud service to store structured, semi-structured or unstructured data produced from applications including social networks, relational data, sensors, videos, web apps, mobile or desktop devices. A single account can store trillions of files where a single file can be greater than a petabyte in size. == Analytics == Data Lake Analytics is a parallel on-demand job service. The parallel processing system is based on Microsoft Dryad. Dryad can represent arbitrary Directed Acyclic Graphs (DAGs) of computation. Data Lake Analytics provides a distributed infrastructure that can dynamically allocate resources so that customers pay for only the services they use. The system uses Apache YARN, the part of Apache Hadoop which governs resource management across clusters. Data Lake Store supports any application that uses the Hadoop Distributed File System (HDFS) interface. == U-SQL == U-SQL is a query language for Data Lake Analytics parallel data transformation and processing programs. It combines SQL and C#: it is and an evolution of the declarative SQL language with native extensibility through user code written in C#. U-SQL uses C# data types and the C# expression language. == Retirement == In 2021, Microsoft announced the 2024 retirement of the original Azure Data Lake Storage, now called "Gen1". The related Azure Data Lake Analytics / U-SQL technologies are also being retired. Azure Data Lake Storage Gen2, an extension of Azure Storage, will continue. The suggested replacement technologies are Azure Synapse Analytics and Apache Spark.

Outline of brain mapping

The following outline is provided as an overview of and topical guide to brain mapping: Brain mapping – set of neuroscience techniques predicated on the mapping of (biological) quantities or properties onto spatial representations of the (human or non-human) brain resulting in maps. Brain mapping is further defined as the study of the anatomy and function of the brain and spinal cord through the use of imaging (including intra-operative, microscopic, endoscopic and multi-modality imaging), immunohistochemistry, molecular and optogenetics, stem cell and cellular biology, engineering (material, electrical and biomedical), neurophysiology and nanotechnology. == Broad scope == History of neuroscience History of neurology Brain mapping Human brain Neuroscience Nervous system. === The neuron doctrine === Neuron doctrine – A set of carefully constructed elementary set of observations regarding neurons. For more granularity, more current, and more advanced topics, see the cellular level section Asserts that neurons fall under the broader cell theory, which postulates: All living organisms are composed of one or more cells. The cell is the basic unit of structure, function, and organization in all organisms. All cells come from preexisting, living cells. The Neuron doctrine postulates several elementary aspects of neurons: The brain is made up of individual cells (neurons) that contain specialized features such as dendrites, a cell body, and an axon. Neurons are cells differentiable from other tissues in the body. Neurons differ in size, shape, and structure according to their location or functional specialization. Every neuron has a nucleus, which is the trophic center of the cell (The part which must have access to nutrition). If the cell is divided, only the portion containing the nucleus will survive. Nerve fibers are the result of cell processes and the outgrowths of nerve cells. (Several axons are bound together to form one nerve fibril. See also: Neurofilament. Several nerve fibrils then form one large nerve fiber. Myelin, an electrical insulator, forms around selected axons. Neurons are generated by cell division. Neurons are connected by sites of contact and not via cytoplasmic continuity. (A cell membrane isolates the inside of the cell from its environment. Neurons do not communicate via direct cytoplasm to cytoplasm contact.) Law of dynamic polarization. Although the axon can conduct in both directions, in tissue there is a preferred direction of transmission from cell to cell. Elements added later to the initial Neuron doctrine A barrier to transmission exists at the site of contact between two neurons that may permit transmission. (Synapse) Unity of transmission. If a contact is made between two cells, then that contact can be either excitatory or inhibitory, but will always be of the same type. Dale's law, each nerve terminal releases a single type of neurotransmitter. Some of the basic postulates in the Neuron doctrine have been subsequently questioned, refuted, or updated. See the cellular level section topics for additional information. === Map, atlas, and database projects === Brain Activity Map Project – 2013 NIH $3 billion project to map every neuron in the human brain in ten years, based upon the Human Genome Project. NIH Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative [1] Community outreach site for above where the public may comment [2] Human Brain Project (EU) – 1 billion euro, 10-year project to simulate the human brain with supercomputers. BigBrain A high-resolution 3D atlas of the human brain created as part of the HBP. Human Connectome Project – 2009 NIH $30 million project to build a network map of the human brain, including structural (anatomical) and functional elements. Emphasis included research into dyslexia, autism, Alzheimer's disease, and schizophrenia. See also Connectome a, comprehensive map of neural connections in the brain. Allen Brain Atlas – 2003 $100 million project funded by Paul Allen (Microsoft) BrainMaps – National Institute of Health (NIH) database including 60 terabytes of image scans of primate and non-primates, integrated with information covering structure and function. NeuroNames – Defines the brain in terms of about 550 primary structures (about 850 unique structures) to which all other structures, names, and synonyms are related. About 15,000 neuroanatomical terms are cross indexed, including many synonyms in seven languages. Coverage includes the brain and spinal cord of the four species most frequently studied by neuroscientists: human, macaque (monkey), rat and mouse. The controlled, standardized vocabulary for each structure is located in an unambiguous, strict physical hierarchy, and these terms are selected based on ease of pronunciation, mnemonic value, and frequency of use in recent neuroscientific publications. Relation of each structure to its superstructures and substructures is included. The controlled vocabulary is suitable for uniquely indexing neuroanatomical information in digital databases. Decade of the Brain 1990–1999 promotion by NIH and the Library of Congress "to enhance public awareness of the benefits to be derived from brain research". Communications targeted Members of Congress, staffs, and the general public to promote funding. Talairach Atlas see Jean Talairach Harvard Whole Brain Atlas see Human brain MNI Template see Medical image computing Blue Brain Project and Artificial brain International Consortium for Brain Mapping see Brain Mapping List of neuroscience databases NIH Toolbox National Institute of Health (USA) toolbox for the assessment of neurological and behavioral function Organization for Human Brain Mapping The Organization for Human Brain Mapping (OHBM) is an international society dedicated to using neuroimaging to discover the organization of the human brain. == Imaging and recording systems == This section covers imaging and recording systems. The general section covers history, neuroimaging, and techniques for mapping specific neural connections. The specific systems section covers the various specific technologies, including experimental and widely deployed imaging and recording systems. === General === Most imaging work to date on individual neurons has been conducted outside the brain, typically on large neurons, and has been most frequently destructive. New techniques are however rapidly emerging. Search on "Single neuron imaging" and see related topics: Biological neuron model, Single-unit recording, Neural oscillation, Computational neuroscience. dMRI (above) is also promising in non-destructive imaging of single neurons inside the brain. History of neuroimaging (redirects from Brain scanner) Neuroimaging (redirects from Brain function map) Connectomics – mapping technique showing neural connections in a nervous system. === Specific systems === Cortical stimulation mapping Diffusion MRI (dMRI) – includes diffusion tensor imaging (DTI) and diffusion functional MRI (DfMRI). dMRI is a recent breakthrough in brain mapping allowing the visualization of cross connections between different anatomical parts of the brain. It allows noninvasive imaging of white matter fiber structure and in addition to mapping can be useful in clinical observations of abnormalities, including damage from stroke. Electroencephalography (EEG) – uses electrodes on the scalp and other techniques to detect the electrical flow of currents. Electrocorticography – intracranial EEG, the practice of using electrodes placed directly on the exposed surface of the brain to record electrical activity from the cerebral cortex. Electrophysiological techniques for clinical diagnosis Functional magnetic resonance imaging (fMRI) Medical image computing (brain research of leads medical and surgical uses of mapping technology) Neurostimulation (in research stimulation is frequently used in conjunction with imaging) Positron emission tomography (PET) – a nuclear medical imaging technique that produces a three-dimensional image or picture of functional processes in the body. The system detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule. Three-dimensional images of tracer concentration within the body are then constructed by computer analysis. In modern scanners, three dimensional imaging is often accomplished with the aid of a CT X-ray scan performed on the patient during the same session, in the same machine. === Imaging and recording componentry === ==== Electrochemical ==== Haemodynamic response – the rapid delivery of blood to active neuronal tissues. Blood Oxygenation Level Dependent signal (BOLD), corresponds to the concentration of deoxyhemoglobin. The BOLD effect is based on the fact that when neuronal activity is increased in one part of the brain, there is also an increased amount of cerebral blood flow to that area. Functional m

Pocketbook (application)

Pocketbook was a Sydney-based free budget planner and personal finance app launched in 2012. The app helped users setup and manage budgets, track spending and manage bills. As of 2016 Pocketbook claimed to support over 250,000 Australians, in January 2018 that number was 435,000. After being acquired by Zip Co Ltd in 2016, it was announced in 2022 that the app was to be shut down and all user accounts deleted. == History == Pocketbook was founded by Alvin Singh and Bosco Tan in 2012. It was conceived in 2011 in a Wolli Creek apartment as a tool for Alvin and Bosco to take control of their money. In 2013, Pocketbook raised $500,000 from technology fund Tank Stream Ventures, and a group of investors including TV personality David Koch, Geoff Levy, David Shein and Peter Cooper. In September 2016 Digital retail finance and payment industry player zipMoney (now trading as Zip Co Limited) acquired Pocketbook in a $7.5m deal == Features == The app synced with the bank account of users and would organize spending into different categories. Users could also be reminded of bill payments, analyse spending and set spending limits. They can also be alerted of fraudulent transactions and deductions. The app employs security measures like end to end encryption, CloudFlare protection, fraud detection, identity protection etc. Pocketbook was available via web and mobile version. == Awards == Personal Finance Innovator of the Year by Fintech Business Awards 2017 Innovator of the Year by OPTUS MyBusiness Awards 2017 Best Finance App of 2016 by Australian Fintech Best Personal Finance App: Pocketbook won the 2016 Finder Innovation Awards, presented at a gala dinner hosted by media personality and The New Inventors presenter James O'Loghlin. Best Mobile App of the Year Winner: StartCon hosted the first annual Australasian Startup Awards. Over 200 nominations in 14 categories and an overall winner were reviewed, and winners were determined by public voting, with over 63,000 votes in total. Best New Startup 2014 by StartupSmart. Finalist in the SWIFT Innotribe startup competition in Dubai in 2013.

Arabic Ontology

Biopython

Azure Data Lake

Outline of brain mapping

Pocketbook (application)

Outline of brain mapping

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