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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
Proximedia Group
Proximedia Group is a Belgian media group. == History == Proximedia Belgium was founded in 1998, by Fabrice Wuyts and Eric Glachant. The company specializes in providing websites for SMEs. The Proximedia Group SA was founded in 1999 and became the coordinating organization of Proximedia Belgium, Online, Bizbook Channel, Globule Bleu bvba, Click+, Proximedia France, Proximedia Nederland, and Proximedia Spain. The Proximedia Group has been listed at the Free Market of Euronext Brussels since 2005. In 2007, the Proximedia Group founded the Bizbook Channel. This branch specialized in creating corporate videos. In 2008, Proximedia SA took over the web agency Globule Bleu. The following year, Proximedia launched the brand BeUP. They were also elected ‘Enterprise of The Year 2009’ by Ernst & Young. Proximedia launched two new services in 2011: Videobiz and Promobook. In 2012, the Bizbook Channel was launched. Proximedia was acquired by Publicis Groupe S.A. in July 2014. == Branches == Proximedia Belgium: the oldest branch of the Proximedia Group. It makes websites and provides support for their customers. Similar branches are Proximedia France and Proximedia Nederland. Batibouw +: specialized in bringing contractors and clients together. Bizbook Channel: specialized in creating corporate videos for SMEs. Click+: offers the management of Google AdWords campaigns. This contains advertising in Google's search results. Globule Bleu: specialized in digital campaigns for larger companies or organisations. Online: an Internet Service Provider (ISP) that provides internet access, domain names, hosting of websites and data centers, email service, etc. Bizbook: an online guestbook where users can post reviews on products and services of a company. Promobook: an online service which can be used to print promotions and coupons. == Key figures == == Sale tactics and lawsuits == There are a lot of websites, forums and blogs that warn for Proximedia. This is because of the long duration of the contract, the inability to terminate the contract and the alleged aggressive approach of Proximedia and the alleged low quality of service that Proximedia offers. Also, there are a lot of lawsuits every month, some of which are customers that wish to terminate the contract, others that allege Proximedia of misguiding. List of some example lawsuits: Mitigation of contractual termination compensation on the basis of article 6:248 paragraph 2 of the Dutch Civil Code A clause on the basis of which a termination fee is claimed can be considered a penalty clause. Mitigation of the penalty based on article 6:94 of the Dutch Civil Code? Performance claim rejected; successful appeal to breach of contract; dissolution; restitution claim awarded. Agreement for IT services. Contents of the agreement. No reflex effect of the Door-to-Door Sales Act for small entrepreneurs. Implementation Act of the Consumer Rights Directive. Breach of contract? Unreasonably onerous clause? Cassation: ECLI:NL:HR:2016:996, (Partial) annulment with referral. Final judgment: ECLI:NL:GHSHE:2014:4228 Error. Reflex effect of the unfair commercial practices law? Compelling evidentiary force of written agreement. (No summary provided by court) Proximedia case. No valid defense against the claim concerning a number of monthly invoices. Article 7.1 of the agreement (containing a termination fee) is a general term in the sense of article 6:231 introductory text and under a of the Dutch Civil Code. No "reflex effect" of article 6:237 introductory text and under i of the Dutch Civil Code. Insufficiently argued why article 7.1 would be unreasonably onerous in the sense of article 6:233 of the Dutch Civil Code and that granting the claim would be unacceptable according to standards of reasonableness and fairness. Termination fee is not a penalty in the sense of article 6:91 of the Dutch Civil Code. A retailer (sole proprietorship) is approached by a representative of a company and enters into an "agreement for IT services" with a term of four years, which includes a dissolution fee of 60% of the not yet due monthly payments. The retailer is instructed to prove that, at the time of entering the agreement, the company promised him that he could terminate the agreement without any further obligations if he terminated his business. The retailer is considered to have succeeded in the burden of proof, and the company's claim for payment of the dissolution fee is rejected.
Mixvoip
Mixvoip S.A. is a Luxembourg-based telecommunications service provider founded in 2008. The company offers IP telephony, high-speed Internet connectivity, and IT solutions to businesses and individuals. == Company history == In November 2017, Mixvoip expanded its operations to Belgium and Germany. At the beginning of 2019, the company acquired the telecommunications provider Voipgate. In December 2019, Mixvoip was named Telecom Company of the Year at the Luxembourg ICT Awards 2019 organized by Farvest and IT One. A 2024 article in Duke described the company's transition during the 2010s from traditional telephony services to cloud-based communication platforms. In the end of 2024, the ILR published the statistics about electronic communications in Luxembourg, including Mixvoip in the fix telephony section. In July 2025, Mixvoip acquired Crossing Telecom. In 2026, Mixvoip acquired Nomado's portfolio.
COVFEFE Act
The Communications Over Various Feeds Electronically for Engagement Act (COVFEFE Act), House Bill H.R. 2884, was introduced in the United States House of Representatives on June 12, 2017, during the 115th United States Congress. The bill was intended to amend the Presidential Records Act to preserve Twitter posts and other social media interactions of the President of the United States and require the National Archives to store such items. H.R. 2884 was assigned to the House Oversight and Reform Committee for consideration. While in committee, there were no roll call votes related to the bill. The bill died in committee. U.S. Representative Mike Quigley, Democrat of Illinois, introduced the legislation due to Donald Trump's routine use of Twitter, stating "In order to maintain public trust in government, elected officials must answer for what they do and say; this includes 140-character tweets. If the president is going to take to social media to make sudden public policy proclamations, we must ensure that these statements are documented and preserved for future reference". If enacted, the bill "would bar the prolifically tweeting president from deleting his posts, as he has sometimes done". The COVFEFE Act would have also treated a president's personal social media accounts (e.g., Trump's "@realDonaldTrump" Twitter account) the same as official social media accounts (e.g., the "@POTUS" Twitter account). == Background == The bill title refers to "covfefe", a word in a May 31, 2017 tweet that Trump sent at 12:06 AM EDT, reading "Despite the constant negative press covfefe". This incomplete tweet was liked and retweeted hundreds of thousands of times, making it one of the most popular tweets of 2017, as people speculated on its meaning. The tweet was deleted at 5:48 AM EDT. At 6:09 AM EDT, Trump's account tweeted "Who can figure out the true meaning of 'covfefe' ??? Enjoy!" During the May 31 White House press briefing, Hunter Walker of Yahoo! News asked White House press secretary Sean Spicer about the tweet and if there was any concern about the president sending out incoherent tweets that stay up for hours. Spicer responded, "I think the president and a small group of people know exactly what he meant" and offered no other explanation. This unexpected response spawned additional media attention and criticism for its cryptic meaning, with commentators unsure whether or not Spicer was joking. Callum Borchers of The Washington Post's The Fix noted that the Trump administration deliberately responded in a way that encouraged the media and the public to focus on covfefe instead of other controversies like the Russia investigation, resignation of White House communications director Michael Dubke, or U.S.-Germany relations. == Legal significance of Trump's tweeting == Trump's tweets have been legally significant in the past. White House Press Secretary Sean Spicer stated that Trump's tweets are "considered official statements by the President of the United States". Some of his tweets have contradicted his agenda by undercutting or contradicting statements of public officials as well as the arguments of U.S. Department of Justice attorneys seeking to defend Trump's decisions in court. A federal appellate court cited one of Trump's tweets in upholding a lower court's order blocking Trump's Executive Order 13780 from going into effect in 2017. Courts have been clear that Twitter statements can be used as evidence of intent. Before Trump's "@realDonaldTrump" Twitter account was suspended, he blocked a number of users, preventing them from viewing his tweets or posting public replies. A group associated with Columbia University filed a lawsuit on behalf of blocked users, called Knight First Amendment Institute v. Trump. Plaintiffs successfully argued that @realDonaldTrump reply threads constituted a "designated public forum" akin to a public meeting, and therefore blocking users based on their political viewpoints violated their constitutional right to freedom of speech. The Second Circuit upheld this ruling on July 9, 2019. Regardless of the failure of the bill, Trump's tweets have been archived in accordance with the Presidential and Federal Records Act Amendments of 2014.
Vanish (computer science)
Vanish was a project to "give users control over the lifetime of personal data stored on the web." It was led by Roxana Geambasu at the University of Washington. The project proposed to allow a user to enter information to send across the internet, thereby relinquishing control of it. However, the user can include an "expiration date," after which the information is no longer usable by anyone who may have a copy of it, even the creator. The Vanish approach was found to be vulnerable to a Sybil attack and thus insecure by a team called Unvanish from the University of Texas, University of Michigan, and Princeton. == Theory == Vanish acts by automating the encryption of information entered by the user with an encryption key that is unknown to the user. Along with the information the user enters, the user also enters metadata concerning how long the information should remain available. The system then encrypts the information but does not store either the encryption key or the original information. Instead, it breaks up the decryption key into smaller components that are disseminated across distributed hash tables, or DHTs, via the Internet. The DHTs refresh information within their nodes on a set schedule unless configured to make the information persistent. The time delay entered by the user in the metadata controls how long the DHTs should allow the information to persist, but once that time period is over, the DHTs will reuse those nodes, making the information about the decryption stored irretrievable. As long as the decryption key may be reassembled from the DHTs, the information is retrievable. However, once the period entered by the user has lapsed, the information is no longer recoverable, as the user never possessed the decryption key. == Implementation == Vanish currently exists as a Firefox plug-in which allows a user to enter text into either a standard Gmail email or Facebook message and choose to send the message via Vanish. The message is then encrypted and sent via the normal networking pathways through the cloud to the recipient. The recipient must have the same Firefox plug-in to decrypt the message. The plugin accesses BitTorrent DHTs, which have 8-hour lifespans. This means the user may select an expiration date for the message in increments of 8 hours. After the expiration of the user-defined time span, the information in the DHT is overwritten, thereby eliminating the key. While both the user and recipient may have copies of the original encrypted message, the key used to turn it back into plain text is now gone. Although this particular instance of the data has become inaccessible, it's important to note that the information can always be saved by other means before expiration (copied or even via screen shots) and published again.
Digital intermediate
Digital intermediate (DI) is a motion picture finishing process which classically involves digitizing a motion picture and manipulating the color and other image characteristics. == Definition and overview == A digital intermediate often replaces or augments the photochemical timing process and is usually the final creative adjustment to a movie before distribution in theaters. It is distinguished from the telecine process in which film is scanned and color is manipulated early in the process to facilitate editing. However the lines between telecine and DI are continually blurred and are often executed on the same hardware by colorists of the same background. These two steps are typically part of the overall color management process in a motion picture at different points in time. A digital intermediate is also customarily done at higher resolution and with greater color fidelity than telecine transfers. Although originally used to describe a process that started with film scanning and ended with film recording, digital intermediate is also used to describe color correction and color grading and even final mastering when a digital camera is used as the image source and/or when the final movie is not output to film. This is due to recent advances in digital cinematography and digital projection technologies that strive to match film origination and film projection. In traditional photochemical film finishing, an intermediate is produced by exposing film to the original camera negative. The intermediate is then used to mass-produce the films that get distributed to theaters. Color grading is done by varying the amount of red, green, and blue light used to expose the intermediate. The digital intermediate process uses digital tools to color grade, which allows for much finer control of individual colors and areas of the image, and allows for the adjustment of image structure (grain, sharpness, etc.). The intermediate for film reproduction can then be produced by means of a film recorder. The physical intermediate film that is a result of the recording process is sometimes also called a digital intermediate, and is usually recorded to internegative (IN) stock, which is inherently finer-grain than original camera negative (OCN). One of the key technical achievements that made the transition to DI possible was the use of 3D look-up tables, which could be used to mimic how the digital image would look once it was printed onto release print stock. This removed a large amount of guesswork from the film-making process, and allowed greater freedom in the colour grading process while reducing risk. The digital master is often used as a source for a DCI-compliant distribution of the motion picture for digital projection. For archival purposes, the digital master created during the digital intermediate process can be recorded to very stable high dynamic range yellow-cyan-magenta (YCM) separations on black-and-white film with an expected 100-year or longer life. While still subject to the natural degradation of any analog chemical master, this archival format, long used in the industry prior to the invention of DI, was considered valuable for providing an archival medium that is independent of changes in digital data recording technologies and file formats that might otherwise render digitally archived material unreadable in the long term. A "film intermediate" is an analog variation of a digital intermediate, where a project shot on digital video is printed onto film stock and transferred back to digital video to emulate film. The term was coined after it was used on the Oscar-winning 2012 short film "Curfew". The process was also used on the films Dune (2021) and The Batman (2022). == History == Telecine tools to electronically capture film images are nearly as old as broadcast television, but the resulting images were widely considered unsuitable for exposing back onto film for theatrical distribution. Film scanners and recorders with quality sufficient to produce images that could be inter-cut with regular film began appearing in the 1970s, with significant improvements in the late 1980s and early 1990s. During this time, digitally processing an entire feature-length film was impractical because the scanners and recorders were extremely slow and the image files were too large compared to computing power available. Instead, individual shots or short sequences were processed for visual effects. In 1992, Visual Effects Supervisor/Producer Chris F. Woods broke through several "techno-barriers" in creating a digital studio to produce the visual effects for the 1993 release Super Mario Bros. It was the first feature film project to digitally scan a large number of VFX plates (over 700) at 2K resolution. It was also the first film scanned and recorded at Kodak's just launched Cinesite facility in Hollywood. This project based studio was the first feature film to use Discreet Logic's (now Autodesk) Flame and Inferno systems, which enjoyed early dominance as high resolution / high performance digital compositing systems. Digital film compositing for visual effects was immediately embraced, while optical printer use for VFX declined just as quickly. Chris Watts further revolutionized the process on the 1998 feature film Pleasantville, becoming the first visual effects supervisor for New Line Cinema to scan, process, and record the majority of a feature-length, live-action, Hollywood film digitally. The first Hollywood film to utilize a digital intermediate process from beginning to end was O Brother, Where Art Thou? in 2000 and in Europe it was Chicken Run released that same year. The process rapidly caught on in the mid-2000s. Around 50% of Hollywood films went through a digital intermediate in 2005, increasing to around 70% by mid-2007. This is due not only to the extra creative options the process affords film makers but also the need for high-quality scanning and color adjustments to produce movies for digital cinema. == Milestones == 1990: The Rescuers Down Under – First feature-length film to be entirely recorded to film from digital files; in this case animation assembled on computers using Walt Disney Feature Animation and Pixar's CAPS system. 1992: Visual effects supervisor and producer Chris F. Woods creates a VFX studio to produce the visual effects for the 1993 film Super Mario Bros. It was the first 35mm feature film to digitally scan a large number of VFX plates (over 700) at 2K resolution, as well as to output the finished VFX to 35mm negative at 2K. 1993: Snow White and the Seven Dwarfs – First film to be entirely scanned to digital files, manipulated, and recorded back to film at 4K resolution. The restoration project was done entirely at 4K resolution and 10-bit color depth using the Cineon system to digitally remove dirt and scratches and restore faded colors. 1998: Pleasantville – The first time the majority of a new feature film was scanned, processed, and recorded digitally. The black-and-white meets color world portrayed in the movie was filmed entirely in color and selectively desaturated and contrast adjusted digitally. The work was done in Los Angeles by Cinesite utilizing a Spirit DataCine for scanning at 2K resolution and a MegaDef color correction system from UK Company Pandora International 1998: Zingo - The first feature film to use digital color correction via digital intermediate in its entirety. The work was performed at the Digital Film Lab in Copenhagen, using a Spirit Datacine to transfer the entire film to digital files at 2K resolution. The digital intermediate process was also used to perform a digital blowup of the film's original Super 16 source format to a 35mm output. 1999: Pacific Ocean Post Film, a team led by John McCunn and Greg Kimble used Kodak film scanners & laser film printer, Cineon software as well as proprietary tools to rebuild and repair the first two reels of the 1968 Beatles' film Yellow Submarine for re-release. 1999: Star Wars: Episode I – The Phantom Menace - Industrial Light & Magic (ILM) scanned the entirety of the visual effects-laden film for the purposes of digital enhancement and the integration of thousands of separately filmed elements with computer generated characters and environments. Outside of the approximately 2000 effects shots that were digitally manipulated, the remaining 170 non-effects shots were also scanned for continuity. However, after the digital shots were manipulated at ILM, they were filmed out individually and sent to Deluxe Labs where they were processed and color timed photochemically. 2000: Sorted - The first feature-length, color 35mm motion picture to fully utilize the digital intermediate process in its entirety from inception to completion. The film was produced at Wave Pictures' digital intermediate film facility in London, England. It was scanned at 2K resolution with 8 bits color depth per color / per pixel using a pin registered, liquid gate Oxberry