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

Truth discovery

Truth discovery (also known as truth finding) is the process of choosing the actual true value for a data item when different data sources provide conflicting information on it. Several algorithms have been proposed to tackle this problem, ranging from simple methods like majority voting to more complex ones able to estimate the trustworthiness of data sources. Truth discovery problems can be divided into two sub-classes: single-truth and multi-truth. In the first case only one true value is allowed for a data item (e.g birthday of a person, capital city of a country). While in the second case multiple true values are allowed (e.g. cast of a movie, authors of a book). Typically, truth discovery is the last step of a data integration pipeline, when the schemas of different data sources have been unified and the records referring to the same data item have been detected. == General principles == The abundance of data available on the web makes more and more probable to find that different sources provide (partially or completely) different values for the same data item. This, together with the fact that we are increasing our reliance on data to derive important decisions, motivates the need of developing good truth discovery algorithms. Many currently available methods rely on a voting strategy to define the true value of a data item. Nevertheless, recent studies, have shown that, if we rely only on majority voting, we could get wrong results even in 30% of the data items. The solution to this problem is to assess the trustworthiness of the sources and give more importance to votes coming from trusted sources. Ideally, supervised learning techniques could be exploited to assign a reliability score to sources after hand-crafted labeling of the provided values; unfortunately, this is not feasible since the number of needed labeled examples should be proportional to the number of sources, and in many applications the number of sources can be prohibitive. == Single-truth vs multi-truth discovery == Single-truth and multi-truth discovery are two very different problems. Single-truth discovery is characterized by the following properties: only one true value is allowed for each data item; different values provided for a given data item oppose to each other; values and sources can either be correct or erroneous. While in the multi-truth case the following properties hold: the truth is composed by a set of values; different values could provide a partial truth; claiming one value for a given data item does not imply opposing to all the other values; the number of true values for each data item is not known a priori. Multi-truth discovery has unique features that make the problem more complex and should be taken into consideration when developing truth-discovery solutions. The examples below point out the main differences of the two methods. Knowing that in both examples the truth is provided by source 1, in the single truth case (first table) we can say that sources 2 and 3 oppose to the truth and as a result provide wrong values. On the other hand, in the second case (second table), sources 2 and 3 are neither correct nor erroneous, they instead provide a subset of the true values and at the same time they do not oppose the truth. == Source trustworthiness == The vast majority of truth discovery methods are based on a voting approach: each source votes for a value of a certain data item and, at the end, the value with the highest vote is select as the true one. In the more sophisticated methods, votes do not have the same weight for all the data sources, more importance is indeed given to votes coming from trusted sources. Source trustworthiness usually is not known a priori but estimated with an iterative approach. At each step of the truth discovery algorithm the trustworthiness score of each data source is refined, improving the assessment of the true values that in turn leads to a better estimation of the trustworthiness of the sources. This process usually ends when all the values reach a convergence state. Source trustworthiness can be based on different metrics, such as accuracy of provided values, copying values from other sources and domain coverage. Detecting copying behaviors is very important, in fact, copy allows to spread false values easily making truth discovery very hard, since many sources would vote for the wrong values. Usually systems decrease the weight of votes associated to copied values or even don’t count them at all. == Single-truth methods == Most of the currently available truth discovery methods have been designed to work well only in the single-truth case. Below are reported some of the characteristics of the most relevant typologies of single-truth methods and how different systems model source trustworthiness. === Majority voting === Majority voting is the simplest method, the most popular value is selected as the true one. Majority voting is commonly used as a baseline when assessing the performances of more complex methods. === Web-link based === These methods estimate source trustworthiness exploiting a similar technique to the one used to measure authority of web pages based on web links. The vote assigned to a value is computed as the sum of the trustworthiness of the sources that provide that particular value, while the trustworthiness of a source is computed as the sum of the votes assigned to the values that the source provides. === Information-retrieval based === These methods estimate source trustworthiness using similarity measures typically used in information retrieval. Source trustworthiness is computed as the cosine similarity (or other similarity measures) between the set of values provided by the source and the set of values considered true (either selected in a probabilistic way or obtained from a ground truth). === Bayesian based === These methods use Bayesian inference to define the probability of a value being true conditioned on the values provided by all the sources. P ( v ∣ ψ ( o ) ) = P ( ψ ( o ) ∣ v ) ⋅ P ( v ) P ( ψ ( o ) ) {\displaystyle P(v\mid \psi (o))={\frac {P(\psi (o)\mid v)\cdot P(v)}{P(\psi (o))}}} where v {\displaystyle \textstyle v} is a value provided for a data item o {\displaystyle \textstyle o} and ψ ( o ) {\displaystyle \textstyle \psi (o)} is the set of the observed values provided by all the sources for that specific data item. The trustworthiness of a source is then computed based on the accuracy of the values that provides. Other more complex methods exploit Bayesian inference to detect copying behaviors and use these insights to better assess source trustworthiness. == Multi-truth methods == Due to its complexity, less attention has been devoted to the study of the multi-truth discovery Below are reported two typologies of multi-truth methods and their characteristics. === Bayesian based === These methods use Bayesian inference to define the probability of a group of values being true conditioned on the values provided by all the data sources. In this case, since there could be multiple true values for each data item, and sources can provide multiple values for a single data item, it is not possible to consider values individually. An alternative is to consider mappings and relations between set of provided values and sources providing them. The trustworthiness of a source is then computed based on the accuracy of the values that provides. More sophisticated methods also consider domain coverage and copying behaviors to better estimate source trustworthiness. === Probabilistic Graphical Models based === These methods use probabilistic graphical models to automatically define the set of true values of given data item and also to assess source quality without need of any supervision. == Applications == Many real-world applications can benefit from the use of truth discovery algorithms. Typical domains of application include: healthcare, crowd/social sensing, crowdsourcing aggregation, information extraction and knowledge base construction. Truth discovery algorithms could be also used to revolutionize the way in which web pages are ranked in search engines, going from current methods based on link analysis like PageRank, to procedures that rank web pages based on the accuracy of the information they provide.

Kruskal count

The Kruskal count (also known as Kruskal's principle, Dynkin–Kruskal count, Dynkin's counting trick, Dynkin's card trick, coupling card trick or shift coupling) is a probabilistic concept originally demonstrated by the Russian mathematician Evgenii Borisovich Dynkin in the 1950s or 1960s discussing coupling effects and rediscovered as a card trick by the American mathematician Martin David Kruskal in the early 1970s as a side-product while working on another problem. It was published by Kruskal's friend Martin Gardner and magician Karl Fulves in 1975. This is related to a similar trick published by magician Alexander F. Kraus in 1957 as Sum total and later called Kraus principle. Besides uses as a card trick, the underlying phenomenon has applications in cryptography, code breaking, software tamper protection, code self-synchronization, control-flow resynchronization, design of variable-length codes and variable-length instruction sets, web navigation, object alignment, and others. == Card trick == The trick is performed with cards, but is more a magical-looking effect than a conventional magic trick. The magician has no access to the cards, which are manipulated by members of the audience. Thus sleight of hand is not possible. Rather the effect is based on the mathematical fact that the output of a Markov chain, under certain conditions, is typically independent of the input. A simplified version using the hands of a clock performed by David Copperfield is as follows. A volunteer picks a number from one to twelve and does not reveal it to the magician. The volunteer is instructed to start from 12 on the clock and move clockwise by a number of spaces equal to the number of letters that the chosen number has when spelled out. This is then repeated, moving by the number of letters in the new number. The output after three or more moves does not depend on the initially chosen number and therefore the magician can predict it.

List of network buses

List of electrical characteristics of single collision domain segment "slow speed" network buses: The number of nodes can be limited by either number of available addresses or bus capacitance. None of the above use any analog domain modulation techniques like MLT-3 encoding, PAM-5 etc. PSI5 designed with automation applications in mind is a bit unusual in that it uses Manchester code.

Critical data studies

Critical data studies is the exploration of and engagement with social, cultural, and ethical challenges that arise when working with big data. It is through various unique perspectives and taking a critical approach that this form of study can be practiced. As its name implies, critical data studies draws heavily on the influence of critical theory, which has a strong focus on addressing the organization of power structures. This idea is then applied to the study of data. Interest in this unique field of critical data studies began in 2011 with scholars danah boyd and Kate Crawford posing various questions for the critical study of big data and recognizing its potential threatening impacts on society and culture. It was not until 2014, and more exploration and conversations, that critical data studies was officially coined by scholars Craig Dalton and Jim Thatcher. They put a large emphasis on understanding the context of big data in order to approach it more critically. Researchers such as David Ribes, Robert Soden, Seyram Avle, Sarah E. Fox, and Phoebe Sengers focus on understanding data as a historical artifact and taking an interdisciplinary approach towards critical data studies. Other key scholars in this discipline include Rob Kitchin and Tracey P. Lauriault who focus on reevaluating data through different spheres. Various critical frameworks that can be applied to analyze big data include Feminist, Anti-Racist, Queer, Indigenous, Decolonial, Anti-Ableist, as well as Symbolic and Synthetic data science. These frameworks help to make sense of the data by addressing power, biases, privacy, consent, and underrepresentation or misrepresentation concerns that exist in data as well as how to approach and analyze this data with a more equitable mindset. == Motivation == In their article in which they coin the term 'critical data studies,' Dalton and Thatcher also provide several justifications as to why data studies is a discipline worthy of a critical approach. First, 'big data' is an important aspect of twenty-first century society, and the analysis of 'big data' allows for a deeper understanding of what is happening and for what reasons. Big data is important to critical data studies because it is the type of data used within this field. Big data does not necessarily refer to a large data set, it can have a data set with millions of rows, but also a data set that just has a wide variety and expansive scope of data with a smaller type of dataset. As well as having whole populations in the data set and not just sample sizes. Furthermore, big data as a technological tool and the information that it yields are not neutral, according to Dalton and Thatcher, making it worthy of critical analysis in order to identify and address its biases. Building off this idea, another justification for a critical approach is that the relationship between big data and society is an important one, and therefore worthy of study. Ribes et. al. argue there is a need for an interdisciplinary understanding of data as a historical artifact as a motivating aspect of critical data studies.The overarching consensus in the Computer-Supported Cooperative Work (CSCW) field, is that people should speak for the data, and not let the data speak for itself. The sources of big data and it’s relationship to varied metadata can be a complicated one, which leads to data disorder and a need for an ethical analysis. Additionally, Iliadis and Russo (2016) have called for studying data assemblages. This is to say, data has innate technological, political, social, and economic histories that should be taken into consideration. Kitchin argues data is almost never raw, and it is almost always cooked, meaning that it is always spoken for by the data scientists utilizing it. Thus, Big Data should be open to a variety of perspectives, especially those of cultural and philosophical nature. Further, data contains hidden histories, ideologies, and philosophies. Big data technology can cause significant changes in society's structure and in the everyday lives of people, and, being a product of society, big data technology is worthy of sociological investigation. Moreover, data sets are almost never completely without any influence. Rather, data are shaped by the vision or goals of those gathering the data, and during the data collection process, certain things are quantified, stored, sorted and even discarded by the research team. A critical approach is thus necessary in order to understand and reveal the intent behind the information being presented.One of these critical approaches has been through feminist data studies. This method applies feminist principles to critical studies and data collecting and analysis. The goal of this is to address the power imbalance in data science and society. According to Catherine D’Ignazio and Lauren F. Klein, a power analysis can be performed by examining power, challenging power, evaluating emotion and embodiment, rethinking binaries and hierarchies, embracing pluralism, considering context, and making labor visible. Feminist data studies is part of the movement towards making data to benefit everyone and not to increase existing inequalities. Moreover, data alone cannot speak for themselves; in order to possess any concrete meaning, data must be accompanied by theoretical insight or alternative quantitative or qualitative research measures. Based on different social topics such as anti-racist data studies, critical data studies give a focus on those social issues concerning data. Specifically in anti-racist data studies they use a classification approach to get representation for those within that community. Desmond Upton Patton and others used their own classification system in the communities of Chicago to help target and reduce violence with young teens on twitter. They had students in those communities help them to decipher the terminology and emojis of these teens to target the language used in tweets that followed with violence outside of the computer screens. This is just one real world example of critical data studies and its application. Dalton and Thatcher argue that if one were to only think of data in terms of its exploitative power, there is no possibility of using data for revolutionary, liberatory purposes. Finally, Dalton and Thatcher propose that a critical approach in studying data allows for 'big data' to be combined with older, 'small data,' and thus create more thorough research, opening up more opportunities, questions and topics to be explored. == Issues and concerns for critical data scholars == Data plays a pivotal role in the emerging knowledge economy, driving productivity, competitiveness, efficiency, sustainability, and capital accumulation. The ethical, political, and economic dimensions of data dynamically evolve across space and time, influenced by changing regimes, technologies, and priorities. Technically, the focus lies on handling, storing, and analyzing vast data sets, utilizing machine learning-based data mining and analytics. This technological advancement raises concerns about data quality, encompassing validity, reliability, authenticity, usability, and lineage. The use of data in modern society brings about new ways of understanding and measuring the world, but also brings with it certain concerns or issues. Data scholars attempt to bring some of these issues to light in their quest to be critical of data. Technical and organizational issues could include the scope of the data set, meaning there is too little or too much data to work with, leading to inaccurate results. It becomes crucial for critical data scholars to carefully consider the adequacy of data volume for their analyses. The quality of the data itself is another facet of concern. The data itself could be of poor quality, such as an incomplete or messy data set with missing or inaccurate data values. This would lead researchers to have to make edits and assumptions about the data itself. Addressing these issues often requires scholars to make edits and assumptions about the data to ensure its reliability and relevance. Data scientists could have improper access to the actual data set, limiting their abilities to analyze it. Linnet Taylor explains how gaps in data can arise when people of varying levels of power have certain rights to their data sources. These people in power can control what data is collected, how it is displayed and how it is analyzed. The capabilities of the research team also play a crucial role in the quality of data analytics. The research team may have inadequate skills or organizational capabilities which leads to the actual analytics performed on the dataset to be biased. This can also lead to ecological fallacies, meaning an assumption is made about an individual based on data or results from a larger group of people. These technical and organizational challenges highlight the complexity of working with data and

Kernel Assisted Superuser

Kernel Assisted Superuser (short: KernelSU) is an alternative method for obtaining root privileges on Android devices. KernelSU implementations are developed as free and open-source software under the terms of the GPLv3 license. == Technical differences == KernelSU differs from other methods in that root access is implemented directly in the kernel. Compared to other root methods that run in userspace, such as Magisk, this has the advantage that commands with su can be executed like normal commands, but still have root privileges. This is not prevented by SELinux or detected by the PlayIntegrity API check, so applications that use it will continue to function. Unlike Magisk, /system/bin/su is a virtual file implemented by hooking system calls with kprobes, and overlayfs is used for systemless modifications to the system partition instead of magic mount. == History == The planning of KernelSU was started in 2018 by developer Jason Donenfeld, also known as XDA user zx2c4. The lack of a root manager app and the difficulty of creating boot images meant that KernelSU was not suitable for productive use, and for a long time this method remained theoretical and could only be used by developers. In 2021, Google launched Generic Kernel Images (GKI for short), which facilitates the creation of a set of device-independent rooted boot images. In response, the developer known on XDA as weishu, who had also worked on projects such as VirtualXposed, adapted KernelSU for GKI-compatible kernels. The adaptation, which was released in January 2023, ensures that any device booting with Linux kernel version 5.10 or higher should be compatible. In addition, the developer also offers a special manager app that, in addition to managing root privileges, also offers overlay-based modding similar to Magisk modules. As of November 2025, 310 developers have contributed to the development of the KernelSU implementation. == Distribution == KernelSU can be installed on all devices that use GKI, as well as on individually supported devices without GKI. Some custom ROMs already have it integrated by default, including ROMs such as CrDroid, Bliss OS, and Evolution X.

AS1 (networking)

AS1 (Applicability Statement 1) is a specification about how to transport structured business-to-business data securely and reliably over the Internet. Security is achieved by using digital certificates and encryption. == AS1 technical overview == The AS1 protocol is based on SMTP and S/MIME. It was the first AS protocol developed and uses signing, encryption and MDN conventions. In other words: Files are sent as "attachments" in a specially coded SMIME email message Messages can be signed, but do not have to be Messages can be encrypted, but do not have to be Messages may request an MDN back if all went well, but do not have to request such a message If the original AS1 message requested an MDN... Upon the receipt of the message and its successful decryption or signature validation (as necessary) a "success" MDN will be sent back to the original sender. This MDN is typically signed but not encrypted. Upon the receipt and successful verification of the signature on the MDN, the original sender will "know" that the recipient got their message (this provides the "Non-repudiation" element of AS1) If there are any problems receiving or interpreting the original AS1 message, a "failed" MDN may be sent back. Like any other AS file transfer, AS1 file transfers typically require both sides of the exchange to trade X.509 certificates and specific "trading partner" names before any transfers can take place.