geWorkbench (genomics Workbench) is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the programming language Java. geWorkbench uses a component architecture. As of 2016, there are more than 70 plug-ins available, providing for the visualization and analysis of gene expression, sequence, and structure data. geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks, one of the 8 National Centers for Biomedical Computing funded through the NIH Roadmap (NIH Common Fund). Many systems and structure biology tools developed by MAGNet investigators are available as geWorkbench plugins. == Features == Computational analysis tools such as t-test, hierarchical clustering, self-organizing maps, regulatory network reconstruction, BLAST searches, pattern-motif discovery, protein structure prediction, structure-based protein annotation, etc. Visualization of gene expression (heatmaps, volcano plot), molecular interaction networks (through Cytoscape), protein sequence and protein structure data (e.g., MarkUs). Integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis. Component integration through platform management of inputs and outputs. Among data that can be shared between components are expression datasets, interaction networks, sample and marker (gene) sets and sequences. Dataset history tracking - complete record of data sets used and input settings. Integration with 3rd party tools such as GenePattern, Cytoscape, and Genomespace. Demonstrations of each feature described can be found at GeWorkbench-web Tutorials. == Versions == geWorkbench is open-source software that can be downloaded and installed locally. A zip file of the released version Java source is also available. Prepackaged installer versions also exist for Windows, Macintosh, and Linux.
Exercism
Exercism is an online, open-source, free coding platform that offers code practice and mentorship on 77 different programming languages. == History == Software developer Katrina Owen created Exercism while she was teaching programming at Jumpstart Labs. The platform was developed as an internal tool to solve the problem of her own students not receiving feedback on the coding problems they were practicing. Katrina put the site publicly online and found that people were sharing it with their friends, practicing together and giving each other feedback. Within 12 months, the site had organically grown to see over 6,000 users had submitted code or feedback, and hundreds of volunteers contribute to the languages or tooling on the platform. In 2016, Jeremy Walker joined as co-founder and CEO. In July 2018, the site was relaunched with a new design and centered around a formal mentoring mode, at which point Katrina stepped back from day-to-day involvement. == Product == In the past, the website differed from other coding platforms by requiring students to download exercises through a command line client, solve the code on their own computers then submit the solution for feedback, at which point they can also view other's solutions to the same problem. Since its second relaunch in 2021, solutions can be edited and submitted through a web editor, though the command line client remains available. Exercism has tracks for 74 programming languages. Among the notable languages taught: ABAP, C, C#, C++, CoffeeScript, Delphi, Elm, Erlang, F#, Gleam, Go, Java, JavaScript, Julia, Kotlin, Objective-C, PHP, Python, Raku, Red, Ruby, Rust, Scala, Swift, and V (Vlang). In 2023, the site launched a "12 in 23" challenge for users to learn the basics of 12 different languages - one per month in 2023. == Open source == The Exercism codebase is open source. In April 2016, it consisted of 50 repositories including website code, API code, command-line code and, most of all, over 40 stand-alone repositories for different language tracks. As of February 2024 Exercism has 14,344 contributors, maintains 366 repositories, and 19,603 mentors.
Richardson–Lucy deconvolution
The Richardson–Lucy algorithm, also known as Lucy–Richardson deconvolution, is an iterative procedure for recovering an underlying image that has been blurred by a known point spread function. It was named after William Richardson and Leon B. Lucy, who described it independently. == Description == When an image is produced using an optical system and detected using photographic film, a charge-coupled device or a CMOS sensor, for example, it is inevitably blurred, with an ideal point source not appearing as a point but being spread out into what is known as the point spread function. Extended sources can be decomposed into the sum of many individual point sources, thus the observed image can be represented in terms of a transition matrix p operating on an underlying image: d i = ∑ j p i , j u j , {\displaystyle d_{i}=\sum _{j}p_{i,j}u_{j},} where u j {\displaystyle u_{j}} is the intensity of the underlying image at pixel j {\displaystyle j} , and d i {\displaystyle d_{i}} is the detected intensity at pixel i {\displaystyle i} . In general, a matrix whose elements are p i , j {\displaystyle p_{i,j}} describes the portion of light from source pixel j that is detected in pixel i. In most good optical systems (or in general, linear systems that are described as shift-invariant) the transfer function p can be expressed simply in terms of the spatial offset between the source pixel j and the observation pixel i: p i , j = P ( i − j ) , {\displaystyle p_{i,j}=P(i-j),} where P ( Δ i ) {\displaystyle P(\Delta i)} is called a point spread function. In that case the above equation becomes a convolution. This has been written for one spatial dimension, but most imaging systems are two-dimensional, with the source, detected image, and point spread function all having two indices. So a two-dimensional detected image is a convolution of the underlying image with a two-dimensional point spread function P ( Δ x , Δ y ) {\displaystyle P(\Delta x,\Delta y)} plus added detection noise. In order to estimate u j {\displaystyle u_{j}} given the observed d i {\displaystyle d_{i}} and a known P ( Δ i x , Δ j y ) {\displaystyle P(\Delta i_{x},\Delta j_{y})} , the following iterative procedure is employed in which the estimate of u j {\displaystyle u_{j}} (called u ^ j ( t ) {\displaystyle {\hat {u}}_{j}^{(t)}} ) for iteration number t is updated as follows: u ^ j ( t + 1 ) = u ^ j ( t ) ∑ i d i c i p i j , {\displaystyle {\hat {u}}_{j}^{(t+1)}={\hat {u}}_{j}^{(t)}\sum _{i}{\frac {d_{i}}{c_{i}}}p_{ij},} where c i = ∑ j p i j u ^ j ( t ) , {\displaystyle c_{i}=\sum _{j}p_{ij}{\hat {u}}_{j}^{(t)},} and ∑ j p i j = 1 {\displaystyle \sum _{j}p_{ij}=1} is assumed. It has been shown empirically that if this iteration converges, it converges to the maximum likelihood solution for u j {\displaystyle u_{j}} . Writing this more generally for two (or more) dimensions in terms of convolution with a point spread function P: u ^ ( t + 1 ) = u ^ ( t ) ⋅ ( d u ^ ( t ) ⊗ P ⊗ P ∗ ) , {\displaystyle {\hat {u}}^{(t+1)}={\hat {u}}^{(t)}\cdot \left({\frac {d}{{\hat {u}}^{(t)}\otimes P}}\otimes P^{}\right),} where the division and multiplication are element-wise, ⊗ {\displaystyle \otimes } indicates a 2D convolution, and P ∗ {\displaystyle P^{}} is the mirrored point spread function, or the inverse Fourier transform of the Hermitian transpose of the optical transfer function. In problems where the point spread function p i j {\displaystyle p_{ij}} is not known a priori, a modification of the Richardson–Lucy algorithm has been proposed, in order to accomplish blind deconvolution. == Derivation == In the context of fluorescence microscopy, the probability of measuring a set of number of photons (or digitalization counts proportional to detected light) m = [ m 0 , … , m K ] {\displaystyle \mathbf {m} =[m_{0},\dots ,m_{K}]} for expected values E = [ E 0 , … , E K ] {\displaystyle \mathbf {E} =[E_{0},\dots ,E_{K}]} for a detector with K + 1 {\displaystyle K+1} pixels is given by P ( m ∣ E ) = ∏ i K Poisson ( E i ) = ∏ i K E i m i e − E i m i ! . {\displaystyle P(\mathbf {m} \mid \mathbf {E} )=\prod _{i}^{K}\operatorname {Poisson} (E_{i})=\prod _{i}^{K}{\frac {E_{i}^{m_{i}}e^{-E_{i}}}{m_{i}!}}.} Since in the context of maximum-likelihood estimation the aim is to locate the maximum of the likelihood function without concern for its absolute value, it is convenient to work with ln ( P ) {\displaystyle \ln(P)} : ln P ( m ∣ E ) = ∑ i K [ ( m i ln E i − E i ) − ln ( m i ! ) ] . {\displaystyle \ln P(\mathbf {m} \mid \mathbf {E} )=\sum _{i}^{K}[(m_{i}\ln E_{i}-E_{i})-\ln(m_{i}!)].} Moreover, since ln ( m i ! ) {\displaystyle \ln(m_{i}!)} is a constant, it does not give any additional information regarding the position of the maximum, so consider α ( m ∣ E ) = ∑ i K [ m i ln E i − E i ] , {\displaystyle \alpha (\mathbf {m} \mid \mathbf {E} )=\sum _{i}^{K}[m_{i}\ln E_{i}-E_{i}],} where α {\displaystyle \alpha } is something that shares the same maximum position as P ( m ∣ E ) {\displaystyle P(\mathbf {m} \mid \mathbf {E} )} . Now consider that E {\displaystyle \mathbf {E} } comes from a ground truth x {\displaystyle \mathbf {x} } and a measurement H {\displaystyle \mathbf {H} } which is assumed to be linear. Then E = H x , {\displaystyle \mathbf {E} =\mathbf {H} \mathbf {x} ,} where a matrix multiplication is implied. This can also be written in the form E m = ∑ n K H m n x n , {\displaystyle E_{m}=\sum _{n}^{K}H_{mn}x_{n},} where it can be seen how H {\displaystyle H} mixes or blurs the ground truth. It can also be shown that the derivative of an element of E {\displaystyle \mathbf {E} } , ( E i ) {\displaystyle (E_{i})} with respect to some other element of x j {\displaystyle x_{j}} can be written as It is easy to see this by writing a matrix H {\displaystyle \mathbf {H} } of, say, 5 × 5 and two arrays E {\displaystyle \mathbf {E} } and x {\displaystyle \mathbf {x} } of 5 elements and check it. This last equation can be interpreted as how much one element of x {\displaystyle \mathbf {x} } , say element i {\displaystyle i} , influences the other elements j ≠ i {\displaystyle j\neq i} (and of course the case i = j {\displaystyle i=j} is also taken into account). For example, in a typical case an element of the ground truth x {\displaystyle \mathbf {x} } will influence nearby elements in E {\displaystyle \mathbf {E} } but not the very distant ones (a value of 0 {\displaystyle 0} is expected on those matrix elements). Now, the key and arbitrary step: x {\displaystyle \mathbf {x} } is not known but may be estimated by x ^ {\displaystyle {\hat {\mathbf {x} }}} . Let's call x ^ old {\displaystyle {\hat {\mathbf {x} }}_{\text{old}}} and x ^ new {\displaystyle {\hat {\mathbf {x} }}_{\text{new}}} the estimated ground truths while using the RL algorithm, where the hat symbol is used to distinguish ground truth from estimator of the ground truth where ∂ ∂ x {\displaystyle {\frac {\partial }{\partial \mathbf {x} }}} stands for a K {\displaystyle K} -dimensional gradient. Performing the partial derivative of α ( m ∣ E ( x ) ) {\displaystyle \alpha (\mathbf {m} \mid \mathbf {E} (\mathbf {x} ))} yields the following expression: ∂ α ( m ∣ E ( x ) ) ∂ x j = ∂ ∂ x j ∑ i K [ m i ln E i − E i ] = ∑ i K [ m i E i ∂ ∂ x j E i − ∂ ∂ x j E i ] = ∑ i K ∂ E i ∂ x j [ m i E i − 1 ] . {\displaystyle {\frac {\partial \alpha (\mathbf {m} \mid \mathbf {E} (\mathbf {x} ))}{\partial x_{j}}}={\frac {\partial }{\partial x_{j}}}\sum _{i}^{K}[m_{i}\ln E_{i}-E_{i}]=\sum _{i}^{K}\left[{\frac {m_{i}}{E_{i}}}{\frac {\partial }{\partial x_{j}}}E_{i}-{\frac {\partial }{\partial x_{j}}}E_{i}\right]=\sum _{i}^{K}{\frac {\partial E_{i}}{\partial x_{j}}}\left[{\frac {m_{i}}{E_{i}}}-1\right].} By substituting (1), it follows that ∂ α ( m ∣ E ( x ) ) ∂ x j = ∑ i K H i j [ m i E i − 1 ] . {\displaystyle {\frac {\partial \alpha (\mathbf {m} \mid \mathbf {E} (\mathbf {x} ))}{\partial x_{j}}}=\sum _{i}^{K}H_{ij}\left[{\frac {m_{i}}{E_{i}}}-1\right].} Note that H j i T = H i j {\displaystyle H_{ji}^{T}=H_{ij}} by the definition of a matrix transpose. And hence Since this equation is true for all j {\displaystyle j} spanning all the elements from 1 {\displaystyle 1} to K {\displaystyle K} , these K {\displaystyle K} equations may be compactly rewritten as a single vectorial equation ∂ α ( m ∣ E ( x ) ) ∂ x = H T [ m E − 1 ] , {\displaystyle {\frac {\partial \alpha (\mathbf {m} \mid \mathbf {E} (\mathbf {x} ))}{\partial \mathbf {x} }}=\mathbf {H} ^{T}\left[{\frac {\mathbf {m} }{\mathbf {E} }}-\mathbf {1} \right],} where H T {\displaystyle \mathbf {H} ^{T}} is a matrix, and m {\displaystyle \mathbf {m} } , E {\displaystyle \mathbf {E} } and 1 {\displaystyle \mathbf {1} } are vectors. Now, as a seemingly arbitrary but key step, let where 1 {\displaystyle \mathbf {1} } is a vector of ones of size K {\displaystyle K} (same as m {\displaystyle \mathbf {m} } , E {\displaystyle \mathbf {E} } and x {\displaystyle \mathbf {x} } ), and the d
WebPlus
Serif WebPlus was a website design program for Microsoft Windows, developed by the software company, Serif. It allows users to design, create and upload their website onto the internet without any knowledge of HTML or other web technologies. Much like Microsoft Word, WebPlus uses WYSIWYG drag and drop editing to add and position text, images and links as they would appear on the finished web page. Once a user has designed their site, WebPlus can preview the site in a web browser before uploading the site using the in-built FTP. The software comes with a variety of pre-designed sample websites containing Filler text like Lorem ipsum, which can be used as a template for quickly designing a site. It also provides drawing tools for creating and editing buttons and web graphics. == Free WebPlus Starter Edition == Previously Serif had made available feature limited Starter Editions of their software, based on older versions, which could be obtained and used free of charge. For WebPlus the final free edition was based on version X5 and this was released in September 2012. This continued to be available from Serif's server until it was withdrawn around March 2016. WebPlus was then only available as a paid-for version X8. == Program Withdrawal == In March 2016, Serif announced that WebPlus X8 would be the final version, and that there were no current plans to design an application to replace it. Sales of WebPlus X8 by Serif were ended around December 2016. In early 2018, Serif announced that Serif Web Resources, hosted on Serif servers and required to implement some advanced web-site functionality in WebPlus created sites, would no longer work after 31 August 2018. In 2018, Serif also shutdown the servers that generated the "Plus" software registration numbers on-line from the product version and the individual generated installation number. Serif revealed the alternative was to use a universal master registration number, which is 881887. This is known to work with post 2003 Serif "Plus" software (e.g. verified to work with PagePlus v5.02). However, later Serif "Plus" software still registers itself automatically if within a certain recent period of a previous Serif software registration on the same PC. == Supported platforms == WebPlus was developed for Microsoft Windows "Win32" graphical desktop interface and is fully compatible with Windows XP, Windows Vista (32/64bit), Windows 7 (32/64bit) and Windows 8. == Features == Web hosting to upload websites to the internet with the address www.sitename.webplus.net and email [email protected]. E-Commerce tool to create online stores with providers such as PayPal. Form wizard generates online forms to collect information from website visitors. Add blogs, forums, hit counters, online polls and content management systems to websites using Smart Objects. Google Maps tool embeds maps and optional navigation markers within a website. Site navigation bars adopt a website's structure providing a tool for navigating around the website. Photo gallery groups a collection of images together and displays them as an animated slideshow. Search engine optimization (SEO) tools optimise a websites search ranking with the likes of Google, Yahoo! and Bing. Collect website metrics such as page popularity and number of website hits using Google Analytics. WebPlus X5 introduced a button studio for creating button graphics. Restrict access to specific pages on a website with a secure member's area. WebPlus automatically converts images and graphics into a web targeted format, optimising them for fast download. Embed YouTube videos within a web page. Add animated effects to a website with Animated GIFs, Animated Marquees or by importing Flash videos. Stream news and information feeds to a website using RSS and podcasts. Automated Site Checker analyses and corrects potential problems with a website. AdSense tool incorporates Google AdSense advertisements into a website In-built FTP transfers files onto a web server, uploading a website to the internet. In-built Basic Photo Editor the PhotoLab can make automatic adjustments and "Quick Fix's" to photos. From X5, WebPlus offers image editing and filters, through its PhotoLab and also provides a dedicated background-removal tool in the form of Cutout Studio. Display images, Flash videos and web pages using animated Lightboxes. Filter Effects can be applied to the graphical objects, giving convincing, realistic effects such as glass, metallic, plastic and other 2D/3D filters. WebPlus also provides QuickShapes for creating button and web graphics. These predefined shapes can be quickly modified with sliders to adjust certain parameters, for example creating rounded rectangles, etc. Shapes include: rectangles, ellipses, stars, spirals, cogs, petals, etc.
Comparison of raster graphics editors
Raster graphics editors can be compared by many variables, including availability. == List == == General information == Basic general information about the editor: creator, company, license, etc. == Operating system support == The operating systems on which the editors can run natively, that is, without emulation, virtual machines or compatibility layers. In other words, the software must be specifically coded for the operation system; for example, Adobe Photoshop for Windows running on Linux with Wine does not fit. == Features == == Color spaces == == File support ==
GeoNetwork opensource
The GeoNetwork opensource (GNOS) project is a free and open source (FOSS) cataloging application for spatially referenced resources. It is a catalog of location-oriented information. == Outline == It is a standardized and decentralized spatial information management environment designed to enable access to geo-referenced databases, cartographic products and related metadata from a variety of sources, enhancing the spatial information exchange and sharing between organizations and their audience, using the capacities of the internet. Using the Z39.50 protocol it both accesses remote catalogs and makes its data available to other catalog services. As of 2007, OGC Web Catalog Service are being implemented. Maps, including those derived from satellite imagery, are effective communicational tools and play an important role in the work of decision makers (e.g., sustainable development planners and humanitarian and emergency managers) in need of quick, reliable and up-to-date user-friendly cartographic products as a basis for action and to better plan and monitor their activities; GIS experts in need of exchanging consistent and updated geographical data; and spatial analysts in need of multidisciplinary data to perform preliminary geographical analysis and make reliable forecasts. == Deployment == The software has been deployed to various organizations, the first being FAO GeoNetwork and WFP VAM-SIE-GeoNetwork, both at their headquarters in Rome, Italy. Furthermore, the WHO, CGIAR, BRGM, ESA, FGDC and the Global Change Information and Research Centre (GCIRC) of China are working on GeoNetwork opensource implementations as their spatial information management capacity. It is used for several risk information systems, in particular in the Gambia. Several related tools are packaged with GeoNetwork, including GeoServer. GeoServer stores geographical data, while GeoNetwork catalogs collections of such data.
Non-separable wavelet
Non-separable wavelets are multi-dimensional wavelets that are not directly implemented as tensor products of wavelets on some lower-dimensional space. They have been studied since 1992. They offer a few important advantages. Notably, using non-separable filters leads to more parameters in design, and consequently better filters. The main difference, when compared to the one-dimensional wavelets, is that multi-dimensional sampling requires the use of lattices (e.g., the quincunx lattice). The wavelet filters themselves can be separable or non-separable regardless of the sampling lattice. Thus, in some cases, the non-separable wavelets can be implemented in a separable fashion. Unlike separable wavelet, the non-separable wavelets are capable of detecting structures that are not only horizontal, vertical or diagonal (show less anisotropy). == Examples == Red-black wavelets Contourlets Shearlets Directionlets Steerable pyramids Non-separable schemes for tensor-product wavelets