Point-in-time recovery (PITR) in the context of computers involves systems, often databases, whereby an administrator can restore or recover a set of data or a particular setting from a time in the past. Note for example Windows's capability to restore operating-system settings from a past date (for instance, before data corruption occurred). Time Machine for macOS provides another example of point-in-time recovery. Once PITR logging starts for a PITR-capable database, a database administrator can restore that database from backups to the state that it had at any time since.
DBGallery
DBGallery, short for Database Gallery, is a cloud-based Software as a Service (SaaS) and on-prem webserver for teams of various sizes. DBGallery enables users to centrally store, manage, catalog, archive, and securely share image, video, and document files. It facilitates version control, detects duplicates, and offers an intuitive and advanced search functionality, making assets easily accessible to all users. It takes advantage of current AI technologies to automatically add significant metadata to images, facilitates custom-trained AI models, and offers bespoke AI features. Additionally, DBGallery provides team management tools, workflow management, an activity audit trail, and other collaborative features that foster a productive environment for both internal and external stakeholders. == History == DBGallery's first public release was December 2007. Since then each year has seen continuous enhancements. 2013 added support for additional non-English languages in its meta-data. 2014 added support for creating custom data fields for tagging and search. In 2015 included the ability to auto-tag images using Reverse Geocoding. 2018 added artificial intelligence (AI) image recognition as a further addition to auto-tagging. March 2020 added complete image collection management via the web (e.g. file and folder drag and drop), a new collection dashboard, custom data layouts, and an improved audit trail. 2021 saw user experience improvements provided by improved styling and performance enhancements. Version 12 was released in October 2021. It added the ability to upload unlimited file sizes and made significant performance improvements for very large collections. June 2022 saw the release of a global duplicate images search. In late 2022, DBGallery began offering significantly reduced cloud storage cost, at a third of its previous prices, which played into its recent high-volume/high-capacity capabilities and its clients' subsequent demand for additional storage. 2023 saw improvements in user and role management, introduced it's mobile app (PWA), and improved custom-trained object detection. Release 14.0 in the spring of 2024 had large sharing improvements and a new find related images feature. Winter 2025's v15 release introduced AI-generated image descriptions, image-to-text, and facial recognition.
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Christopher K. I. Williams
Christopher Kenneth Ingle Williams (born 1960) is a professor at the School of Informatics, University of Edinburgh, working in Artificial intelligence, and particularly the areas of Machine learning and Computer vision. == Education == Williams received a BA in Physics and Theoretical Physics from the University of Cambridge in 1982, followed by Part III Mathematics (1983). He did a MSc in Water Resources at the University of Newcastle-Upon-Tyne, then worked in Lesotho on low-cost sanitation. In 1988, he studied at the Department of Computer Science of the University of Toronto under the supervision of Geoffrey Hinton. He obtained his MSc and PhD both in computer science, in 1990 and 1994, respectively. == Career and research == In 1994, Williams moved to Aston University as a Research Fellow. He became a Lecturer in August 1995. He moved to the University of Edinburgh in July 1998 and became Reader in 2000. He obtained a Personal Chair in Machine Learning in 2005 in the School of Informatics. Williams has been a Fellow of the European Laboratory for Learning and Intelligent Systems (ELLIS) since 2019. Williams' research interests are in machine learning and computer vision. He has worked on new models for understanding time-series and images, and for finding structure in data. He is best known for his work on Gaussian processes and for the book Gaussian Processes for Machine Learning, co-authored with Carl Rasmussen. The book received the 2009 DeGroot Prize of the International Society for Bayesian Analysis. Williams was an organizer of the PASCAL Visual Object Classes (VOC) project (2005–2012) along with Mark Everingham, Luc van Gool, John Winn, and Andrew Zisserman. == Awards and honours == In 2021 Williams was elected a Fellow of the Royal Society of Edinburgh (FRSE).
Multiple sequence alignment
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences. Alignments highlight mutation events such as point mutations (single amino acid or nucleotide changes), insertion mutations and deletion mutations, and alignments are used to assess sequence conservation and infer the presence and activity of protein domains, tertiary structures, secondary structures, and individual amino acids or nucleotides. Multiple sequence alignments require more sophisticated methodologies than pairwise alignments, as they are more computationally complex. Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive. However, heuristic methods generally cannot guarantee high-quality solutions and have been shown to fail to yield near-optimal solutions on benchmark test cases. == Problem statement == Given m {\displaystyle m} sequences S i {\displaystyle S_{i}} , i = 1 , ⋯ , m {\displaystyle i=1,\cdots ,m} similar to the form below: S := { S 1 = ( S 11 , S 12 , … , S 1 n 1 ) S 2 = ( S 21 , S 22 , ⋯ , S 2 n 2 ) ⋮ S m = ( S m 1 , S m 2 , … , S m n m ) {\displaystyle S:={\begin{cases}S_{1}=(S_{11},S_{12},\ldots ,S_{1n_{1}})\\S_{2}=(S_{21},S_{22},\cdots ,S_{2n_{2}})\\\,\,\,\,\,\,\,\,\,\,\vdots \\S_{m}=(S_{m1},S_{m2},\ldots ,S_{mn_{m}})\end{cases}}} A multiple sequence alignment is taken of this set of sequences S {\displaystyle S} by inserting any amount of gaps needed into each of the S i {\displaystyle S_{i}} sequences of S {\displaystyle S} until the modified sequences, S i ′ {\displaystyle S'_{i}} , all conform to length L ≥ max { n i ∣ i = 1 , … , m } {\displaystyle L\geq \max\{n_{i}\mid i=1,\ldots ,m\}} and no values in the sequences of S {\displaystyle S} of the same column consists of only gaps. The mathematical form of an MSA of the above sequence set is shown below: S ′ := { S 1 ′ = ( S 11 ′ , S 12 ′ , … , S 1 L ′ ) S 2 ′ = ( S 21 ′ , S 22 ′ , … , S 2 L ′ ) ⋮ S m ′ = ( S m 1 ′ , S m 2 ′ , … , S m L ′ ) {\displaystyle S':={\begin{cases}S'_{1}=(S'_{11},S'_{12},\ldots ,S'_{1L})\\S'_{2}=(S'_{21},S'_{22},\ldots ,S'_{2L})\\\,\,\,\,\,\,\,\,\,\,\vdots \\S'_{m}=(S'_{m1},S'_{m2},\ldots ,S'_{mL})\end{cases}}} To return from each particular sequence S i ′ {\displaystyle S'_{i}} to S i {\displaystyle S_{i}} , remove all gaps. == Graphing approach == A general approach when calculating multiple sequence alignments is to use graphs to identify all of the different alignments. When finding alignments via graph, a complete alignment is created in a weighted graph that contains a set of vertices and a set of edges. Each of the graph edges has a weight based on a certain heuristic that helps to score each alignment or subset of the original graph. === Tracing alignments === When determining the best suited alignments for each MSA, a trace is usually generated. A trace is a set of realized, or corresponding and aligned, vertices that has a specific weight based on the edges that are selected between corresponding vertices. When choosing traces for a set of sequences it is necessary to choose a trace with a maximum weight to get the best alignment of the sequences. == Alignment methods == There are various alignment methods used within multiple sequence to maximize scores and correctness of alignments. Each is usually based on a certain heuristic with an insight into the evolutionary process. Most try to replicate evolution to get the most realistic alignment possible to best predict relations between sequences. === Dynamic programming === A direct method for producing an MSA uses the dynamic programming technique to identify the globally optimal alignment solution. For proteins, this method usually involves two sets of parameters: a gap penalty and a substitution matrix assigning scores or probabilities to the alignment of each possible pair of amino acids based on the similarity of the amino acids' chemical properties and the evolutionary probability of the mutation. For nucleotide sequences, a similar gap penalty is used, but a much simpler substitution matrix, wherein only identical matches and mismatches are considered, is typical. The scores in the substitution matrix may be either all positive or a mix of positive and negative in the case of a global alignment, but must be both positive and negative, in the case of a local alignment. For n individual sequences, the naive method requires constructing the n-dimensional equivalent of the matrix formed in standard pairwise sequence alignment. The search space thus increases exponentially with increasing n and is also strongly dependent on sequence length. Expressed with the big O notation commonly used to measure computational complexity, a naïve MSA takes O(LengthNseqs) time to produce. To find the global optimum for n sequences this way has been shown to be an NP-complete problem. In 1989, based on Carrillo-Lipman Algorithm, Altschul introduced a practical method that uses pairwise alignments to constrain the n-dimensional search space. In this approach pairwise dynamic programming alignments are performed on each pair of sequences in the query set, and only the space near the n-dimensional intersection of these alignments is searched for the n-way alignment. The MSA program optimizes the sum of all of the pairs of characters at each position in the alignment (the so-called sum of pair score) and has been implemented in a software program for constructing multiple sequence alignments. In 2019, Hosseininasab and van Hoeve showed that by using decision diagrams, MSA may be modeled in polynomial space complexity. === Progressive alignment construction === The most widely used approach to multiple sequence alignments uses a heuristic search known as progressive technique (also known as the hierarchical or tree method) developed by Da-Fei Feng and Doolittle in 1987. Progressive alignment builds up a final MSA by combining pairwise alignments beginning with the most similar pair and progressing to the most distantly related. All progressive alignment methods require two stages: a first stage in which the relationships between the sequences are represented as a phylogenetic tree, called a guide tree, and a second step in which the MSA is built by adding the sequences sequentially to the growing MSA according to the guide tree. The initial guide tree is determined by an efficient clustering method such as neighbor-joining or unweighted pair group method with arithmetic mean (UPGMA), and may use distances based on the number of identical two-letter sub-sequences (as in FASTA rather than a dynamic programming alignment). Progressive alignments are not guaranteed to be globally optimal. The primary problem is that when errors are made at any stage in growing the MSA, these errors are then propagated through to the final result. Performance is also particularly bad when all of the sequences in the set are rather distantly related. Most modern progressive methods modify their scoring function with a secondary weighting function that assigns scaling factors to individual members of the query set in a nonlinear fashion based on their phylogenetic distance from their nearest neighbors. This corrects for non-random selection of the sequences given to the alignment program. Progressive alignment methods are efficient enough to implement on a large scale for many (100s to 1000s) sequences. A popular progressive alignment method has been the Clustal family. ClustalW is used extensively for phylogenetic tree construction, in spite of the author's explicit warnings that unedited alignments should not be used in such studies and as input for protein structure prediction by homology modeling. European Bioinformatics Institute (EMBL-EBI) announced that CLustalW2 will expire in August 2015. They recommend Clustal Omega which performs based on seeded guide trees and HMM profile-profile techniques for protein alignments. An alternative tool for progressive DNA alignments is multiple alignment using fast Fourier transform (MAFFT). Another common progressive alignment method named T-Coffee is slower than Clustal and its derivatives but generally produces more accurate alignments for distantly related sequence sets. T-Coffee calculates pairwise alignments by combining the direct alignment of the pair with indirect alignments that aligns each sequence of the pair to a third sequence. It uses the output from Clustal as well as another local alignment program LALIGN, which finds multiple regions of local alignment between two sequences. The resulting alignment and phylogenetic tree are used as a guide to produce new and more accurate w
Multiple buffering
In computer science, multiple buffering is the use of more than one buffer to hold a block of data, so that a "reader" will see a complete (though perhaps old) version of the data instead of a partially updated version of the data being created by a "writer". It is very commonly used for computer display images. It is also used to avoid the need to use dual-ported RAM (DPRAM) when the readers and writers are different devices. == Description == === Double buffering Petri net === The Petri net in the illustration shows double buffering. Transitions W1 and W2 represent writing to buffer 1 and 2 respectively while R1 and R2 represent reading from buffer 1 and 2 respectively. At the beginning, only the transition W1 is enabled. After W1 fires, R1 and W2 are both enabled and can proceed in parallel. When they finish, R2 and W1 proceed in parallel and so on. After the initial transient where W1 fires alone, this system is periodic and the transitions are enabled – always in pairs (R1 with W2 and R2 with W1 respectively). == Double buffering in computer graphics == In computer graphics, double buffering is a technique for drawing graphics that shows less stutter, tearing, and other artifacts. It is difficult for a program to draw a display so that pixels do not change more than once. For instance, when updating a page of text, it is much easier to clear the entire page and then draw the letters than to somehow erase only the pixels that are used in old letters but not in new ones. However, this intermediate image is seen by the user as flickering. In addition, computer monitors constantly redraw the visible video page (traditionally at around 60 times a second), so even a perfect update may be visible momentarily as a horizontal divider between the "new" image and the un-redrawn "old" image, known as tearing. === Software double buffering === A software implementation of double buffering has all drawing operations store their results in some region of system RAM; any such region is often called a "back buffer". When all drawing operations are considered complete, the whole region (or only the changed portion) is copied into the video RAM (the "front buffer"); this copying is usually synchronized with the monitor's raster beam in order to avoid tearing. Software implementations of double buffering necessarily require more memory and CPU time than single buffering because of the system memory allocated for the back buffer, the time for the copy operation, and the time waiting for synchronization. Compositing window managers often combine the "copying" operation with "compositing" used to position windows, transform them with scale or warping effects, and make portions transparent. Thus, the "front buffer" may contain only the composite image seen on the screen, while there is a different "back buffer" for every window containing the non-composited image of the entire window contents. === Page flipping === In the page-flip method, instead of copying the data, both buffers are capable of being displayed. At any one time, one buffer is actively being displayed by the monitor, while the other, background buffer is being drawn. When the background buffer is complete, the roles of the two are switched. The page-flip is typically accomplished by modifying a hardware register in the video display controller—the value of a pointer to the beginning of the display data in the video memory. The page-flip is much faster than copying the data and can guarantee that tearing will not be seen as long as the pages are switched over during the monitor's vertical blanking interval—the blank period when no video data is being drawn. The currently active and visible buffer is called the front buffer, while the background page is called the back buffer. == Triple buffering == In computer graphics, triple buffering is similar to double buffering but can provide improved performance. In double buffering, the program must wait until the finished drawing is copied or swapped before starting the next drawing. This waiting period could be several milliseconds during which neither buffer can be touched. In triple buffering, the program has two back buffers and can immediately start drawing in the one that is not involved in such copying. The third buffer, the front buffer, is read by the graphics card to display the image on the monitor. Once the image has been sent to the monitor, the front buffer is flipped with (or copied from) the back buffer holding the most recent complete image. Since one of the back buffers is always complete, the graphics card never has to wait for the software to complete. Consequently, the software and the graphics card are completely independent and can run at their own pace. Finally, the displayed image was started without waiting for synchronization and thus with minimum lag. Due to the software algorithm not polling the graphics hardware for monitor refresh events, the algorithm may continuously draw additional frames as fast as the hardware can render them. For frames that are completed much faster than interval between refreshes, it is possible to replace a back buffers' frames with newer iterations multiple times before copying. This means frames may be written to the back buffer that are never used at all before being overwritten by successive frames. Nvidia has implemented this method under the name "Fast Sync". An alternative method sometimes referred to as triple buffering is a swap chain three buffers long. After the program has drawn both back buffers, it waits until the first one is placed on the screen, before drawing another back buffer (i.e. it is a 3-long first in, first out queue). Most Windows games seem to refer to this method when enabling triple buffering. == Quad buffering == The term quad buffering is the use of double buffering for each of the left and right eye images in stereoscopic implementations, thus four buffers total (if triple buffering was used then there would be six buffers). The command to swap or copy the buffer typically applies to both pairs at once, so at no time does one eye see an older image than the other eye. Quad buffering requires special support in the graphics card drivers which is disabled for most consumer cards. AMD's Radeon HD 6000 Series and newer support it. 3D standards like OpenGL and Direct3D support quad buffering. == Double buffering for DMA == The term double buffering is used for copying data between two buffers for direct memory access (DMA) transfers, not for enhancing performance, but to meet specific addressing requirements of a device (particularly 32-bit devices on systems with wider addressing provided via Physical Address Extension). Windows device drivers are a place where the term "double buffering" is likely to be used. Linux and BSD source code calls these "bounce buffers". Some programmers try to avoid this kind of double buffering with zero-copy techniques. == Other uses == Double buffering is also used as a technique to facilitate interlacing or deinterlacing of video signals.
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