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Bayesian Calculator 2.0.2

Bayesian Calculator 2.0.2


Bayesian Calculator is a distinguished and easy to use tool which calculates positive predictive power, given prevalence and test results. more>>

Bayesian Calculator 2.0.2 is a distinguished and easy to use tool which calculates positive predictive power, given prevalence and test results.

Requirements: Mac OS X 10.2 or higher (Universal Binary)

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Added: 2006-11-11 License: Freeware Price:
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Other version of Bayesian Calculator
Bayesian Calculator 2.0Marley W. Watkins - Bayesian Calculator calculates positive predictive power, given prevalence and test results. Bayesian
License:Freeware
Download (2.3MB)
1085 downloads
Added: 2006-11-13
SpamBayes 1.1a2

SpamBayes 1.1a2


SpamBayes - a statistical anti-spam filter more>>
SpamBayes is a tool designed as a statistical (commonly, although a little inaccurately, referred to as Bayesian) anti-spam filter, initially based on the work of Paul Graham.

The major difference between this and other, similar projects is the emphasis on testing newer approaches to scoring messages.

While most anti-spam projects are still working with the original graham algorithm, we found that a number of alternate methods yielded a more useful response. This is documented on the background page.

SpamBayes is not a single application. The core code is a message classifier, however there are several applications available as part of the SpamBayes project which use the classifier in specific contexts.

For the most part, the current crop of applications all operate on the client side of things, however, a number of people have experimented with using SpamBayes on mail servers to classify incoming mail for multiple users. The table below outlines the main applications which are part of the SpamBayes distribution.
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Added: 2007-04-18 License: Freeware Price:
920 downloads
SpamAssassin 3.2.2

SpamAssassin 3.2.2


SpamAssassin is a mail filter which attempts to identify spam using a variety of mechanisms including text analysis more>>
SpamAssassin is a mail filter which attempts to identify spam using a variety of mechanisms including text analysis, Bayesian filtering, DNS blocklists, and collaborative filtering databases.
Once identified, the mail can then be optionally tagged as spam for later filtering using the users own mail user-agent application.
SpamAssassin uses a wide range of heuristic tests on mail headers and body text to identify spam, also known as unsolicited commercial email.
SpamAssassin typically differentiates successfully between spam and non-spam in between 95% and 100% of cases, depending on what kind of mail you get and your training of its Bayesian filter.
Specifically, SpamAssassin has been shown to produce around 0.9% false negatives (spam that was missed) and around 0.1% false positives (ham incorrectly marked as spam). See the rules/STATISTICS*.txt files for more information.
Main features:
- Wide-spectrum: SpamAssassin uses a wide variety of local and network tests to identify spam signatures. This makes it harder for spammers to identify one aspect which they can craft their messages to work around.
- Free software: it is distributed under the same terms and conditions as other popular open-source software packages such as the Apache web server.
- Easy to extend: Anti-spam tests and configuration are stored in plain text, making it easy to configure and add new rules.
- Flexible: SpamAssassin encapsulates its logic in a well-designed, abstract API so it can be integrated anywhere in the email stream. The Mail::SpamAssassin classes can be used on a wide variety of email systems including procmail, sendmail, Postfix, qmail, and many others.
- Easy Configuration: SpamAssassin requires very little configuration; you do not need to continually update it with details of your mail accounts, mailing list memberships, etc. Once classified, site and user-specific policies can then be applied against spam. Policies can be applied on both mail servers and later using the users own mail user-agent application.
Enhancements:
- Releas notes can be read here: http://svn.apache.org/repos/asf/spamassassin/branches/3.2/build/announcements/3.2.0.txt
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Added: 2007-07-27 License: GPL Price:
824 downloads
SpamSieve 2.7.7

SpamSieve 2.7.7


SpamSieve comes to you as a useful tool which helps you be back your inbox by bringing powerful Bayesian spam filtering to popular e-mail clients. more>> <<less
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Added: 2009-10-19 License: update/patch Price: $30.00
downloads
 
Other version of SpamSieve
SpamSieve 2.7.6Michael J Tsai - program that is created to give you back your inbox by bringing powerful Bayesian spam filtering to popular e-mail clients. SpamSieve
Price: $30.00
License:update/patch
Download (5.9MB)
downloads
Added: 2009-09-07
SpamSieve 2.7.5Michael J Tsai - which gives you back your inbox by bringing powerful Bayesian spam filtering to popular e-mail clients. SpamSieve
Price: $30.00
License:update/patch
Download (5.9MB)
downloads
Added: 2009-07-28
Outspring Mail 1.1.1

Outspring Mail 1.1.1


Email client with automation and learning features. more>>

Outspring Mail 1.1.1 is an email program which can help you in various ways. Like offering to reply to certain types of email messages using a response you've previously sent. Or giving you the option to auto-file a message you've read based on how you've filed similar messages in the past. What if you could defer a message from your inbox for a few days or weeks, so that it magically reappears later when you're ready to deal with it? What if this program had an amazing junk mail filter that would leave your inbox devoid of spam? And what if this program was as familiar and easy to use as Apple Mail?

Outspring Mail is the newest email client for Macintosh.This tool can include the best features of existing email programs and coupled them with our patent-pending intelligent functions to create a program that will make your email chores far easier. And since this is a current-generation application, it supports major email protocols including POP, IMAP, SMTP and SSL. It also runs natively on the latest Macintosh computers and OS X Leopard. Demo notes: Launching the program and pressing the DEMO button (instead of entering a serial number) will place the program in demo mode, which is: All functions and features of the program will operate for 10 days. A "This message was sent with Outspring Mail..." tag will be added to all outgoing messages sent with the program. After the 10-day demo period has expired, the program will still work, but the user will not be able to send out mail or receive new mail until reactivated with a serial number provided at purchase.

Major Features:

  1. Unique Features
    • Auto-Filing
    • Auto-Reply
    • Find Similar Messages
    • Reply with Template
    • Message Deferment
    • Message Preview with Intelligent Summary
    • Tabbed Display
    • Resize / Rotate Images
    • Mail Account Icons
  2. Email With A Brain: Outspring Mail ushers in an entirely new category of software to the Macintosh: adaptive intelligent software. By using advanced database analysis and Bayesian logic, the program is able to ascertainImage patterns in the way you reply to and file your mail and make suggestions to assist you with your communications. Think about it...if you frequently reply to an email message that says, "How do I get to your office?" or words to that effect; shouldn't your email program be smart enough to know that you've replied to this same type of message before? And shouldn't it then offer to use one of these replies for the current message? The program also offers a similar technique for filing messages. Once the program has gone through a short learning process of observing your mail filing habits and cross-referencing message content, it will begin to suggest appropriate folders or mailboxes to file messages. Instead of dragging messages to folder icons, you'll be presented with one or more likely destination buttons that will automatically file your mail in an appropriate location.
  3. Message Deferment: Another unique feature of Outspring Mail is a function called Message Deferment. This is much like the "snooze" button on an alarm clock. Many people will receive a message, read it, make a mental note to handle it later and then leave it in their Inbox. ImageAfter a few weeks or months, their Inbox becomes an unmanageable mess. But what if you could instead read the message, decide you don't want to deal with it this week and send it "away" for a week? The deferment feature then moves the message to a special folder and the program waits for the selected amount of time. When that time period has elapsed, Outspring Mail then moves the message back into the Inbox with an indicator reminding you that the message is a deferred message that has been returned.
  4. Intelligent Summary:The product also contains a unique "Intelligent Summary" view. By using advanced summarizing algorithms, this feature allows you to quickly review email by a list of the summarized content, negating the need to open each message to see the heart of that content.
  5. Spam Control:ImageOutspring Mail also contains an advanced spam filter that can eliminate 98% of your incoming junk mail. Having developed a server-side spam blocker for a number of years, Outspring has leveraged this experience into the spam filter which is included with the product.
  6. Data Detectors For Calendar & Address Book: Another useful feature is data detection on incoming messages that link to the Macintosh built in Imagecalendar, iCal. If you receive a message that contains a phrase like, "Let's meet for lunch next Friday...", Outspring Mail will convert the phrase "next Friday" into a hot link. Clicking that link will take you to the iCal entry for the following Friday (based on the send date of the message). This Imagefeature works with literal dates like 1/15/09, May 15, 2008 and also with relative dates like "next Friday", "last Tuesday", etc.
  7. Outspring Mail also links to your Apple address book, so contact data will be displayed within messages (like the contacts photo, if present). Clicking on that contact's image will take you to that entry in the address book.
  8. Easy Transition From Apple Mail & QuickMailImage: Whether you are an existing Apple Mail or QuickMail user, you'll find it easy to import all of your existing email data into Outspring Mail. Our import assistant allows you to select which accounts you wish to import into Outspring Mail while leaving the database of the prior program intact. Import works with both POP and IMAP accounts.
  9. ImageSpell Check Outspring Mail utilizes the the Macintosh system dictionary for spelling, corrections, synonyms and definitions. Misspelled words are highlighted as they are typed, which reduces the need to proof-read your outgoing messages. You can also check the definitions of words by simply control-clicking the word in question. By using the system dictionary, Outspring Mail is compatible with any language supported by OS X.

Enhancements: Bug fixes:

  • Fixed a bug which prevented adding/removing columns in the message list.
  • Fixed missing message headers when switching rapidly between messages.
  • Fixed an issue with demo serial number invalid.


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Added: 2009-07-15 License: update/patch Price: $59.00
14 downloads
JavaPK for Desktop 2.5.1008

JavaPK for Desktop 2.5.1008


JavaPK for Desktop is a really superior and tractable clinical pharmacokinetic (CPK) services (or therapeutic drug monitoring, TDM) computer program for desktop. more>>

JavaPK for Desktop 2.5.1008 is a really superior and tractable clinical pharmacokinetic (CPK) services (or therapeutic drug monitoring, TDM) computer program for desktop.

It not only inherits all functionalities of JavaPK for Mobile Devices, but also has a built- in algorithm of users defined Bayesian model for individualized pharmacokinetic parameter estimation (UDBM) for batch input data. Users can define their own pharmacokinetic prediction models with population PK parameters and then use the defined model to solve batch prediction data or applied the defined model to therapeutic drug monitoring (TDM).

Enhancements:
  • Add the row header and help button to "UDBM""Run Defined Drug Model"
  • Change the appearances of the input and parameter table in UDBM
    -->TDM
  • Update the imported library. (JFreeChart 1.0.0-rc1-->1.0.1)
  • Package the "Valproic_acid" model file in new version.

Requirements: Mac OS X, Java.


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Added: 2006-10-09 License: Free Price:
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Other version of JavaPK for Desktop
JavaPK for Desktop 2.5Devices, but also has a built- in algorithm of users defined Bayesian model for individualized pharmacokinetic parameter estimation (UDBM) for batch input data. Users can define their own pharmacokinetic
License:Freeware
Download (2.4MB)
1112 downloads
Added: 2006-10-09
Boomer 3.1.9

Boomer 3.1.9


Boomer - Non-linear regression app for pharmacokinetic data more>>
BOOMER is a general purpose modeling and simulation program. It provides the estimation of parameter values by non-linear weighted least squares regression or the simulation of complex systems of differential equations.
Parameter estimation can be by normal or Bayesian methods. A comprehensive list of weighting schemes is included. The model to be analyzed can be entered as a system of integrated equations or as a system of differential equations. Differential equations are solved by a classical fourth order Runge-Kutta method, a fourth order Runge-Kutta-Gill method, a four/five Runge-Kutta-Fehlberg method, an Adams predictor-corrector method, or Gears method for stiff equations. Simulation with random error in parameters or data are also possible. A batch run can be repeated many times to assist in Monte Carlo type studies.
Enhancements:
- Fixed a bug that caused a segmentation error with more than 30 adjustable parameters ;-)
- added form feed to output.
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Added: 2006-02-20 License: Freeware Price:
1343 downloads
textkit4j 1.0

textkit4j 1.0


Software that provides a set of tools for text processing more>>
textkit4j 1.0 provides you with a perfect and very useful software which provides a set of tools for text processing such as text extraction and classification. Classification implementations to be implemented in textkit4j include: Bayesian and Statistical (N-gram).

Enhancements: Nothing has changed, just including the whole thing.

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Download (68KB)
Added: 2009-05-08 License: GPL Price: FREE
12 downloads
Quantum Fog 2.0

Quantum Fog 2.0


Quantum Fog - Quantum computer simulator more>>
Quantum Fog can model physical situations that exhibit quantum mechanical behavior.

It is a tool for investigating and discussing quantum measurement problems graphically, in terms of network diagrams called quantum Bayesian nets. It simulates a general purpose quantum computer.
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Added: 2006-10-09 License: Freeware Price:
1112 downloads
ROX Desktop 1.0.2

ROX Desktop 1.0.2


A fast, user friendly desktop which makes extensive use of drag-and-drop more>> SpamSieve gives you back your inbox by bringing powerful Bayesian spam filtering to Mac e-mail clients. it is quick and easy to control SpamSieve from within your mail client, and you can customize how it interacts with the rest of your message sorting rules. Other spam filters get worse over time as spammers adapt to their rules; SpamSieve actually gets better over time as it adapts to your mail. By learning from the very messages that you receive, SpamSieve is able to block nearly all of your spam, without putting your good messages in the spam mailbox.<<less
Download (260KB)
Added: 2009-05-12 License: GPL Price: FREE
204 downloads
Intego Personal Antispam X5 10.5.3

Intego Personal Antispam X5 10.5.3


Intego Personal Antispam X5 10.5.3 is the intelligent spam-fighting tool for Mac OS X, which analyzes your incoming e-mail, determining which messages are spam and which are valid messages. more>>

Intego Personal Antispam X5 10.5.3 is the intelligent spam-fighting tool for Mac OS X, which analyzes your incoming e-mail, determining which messages are spam and which are valid messages. Personal Antispam X5 learns from the e-mail users receive, and regular monthly updates to the program help keep inboxes as spam-free as possible.

In addition to keeping inboxes free of spam, Personal Antispam X5 helps protect against two serious threats: phishing and viruses. Some viruses circulate by e-mail as attachments, and Personal Antispam X5 detects specific types of attachments and moves messages containing them to the spam folder. As for phishing, e-mail scams intended to trick users into logging into web sites and giving up their passwords, account numbers or credit card numbers, Personal Antispam X5 detects and filters these messages in several ways: by the words they contain, the links in phishing messages, and specific types of layout.

Major Features:

  1. Filters e-mail and weeds out spam, placing it in a Spam folder
  2. Filters spam with Bayesian analysis
  3. Filters spam by address, message content, layout and more
  4. Filters spam with a whitelist of users' contacts
  5. Filters spam by developing a blacklist of spammers' addresses
  6. Filters spam by top-level domain; users can exclude specific domains, such as .ru, .cn, .biz and more
  7. Filters messages with incorrect encoding and identifiers
  8. Filters phishing e-mails
  9. Filters attachments for common file names
  10. Trusts contacts in user's Address Book
  11. Trusts ISP's spam headers
  12. Learns from the spam users receive
  13. Learns from legitimate e-mails
  14. Does not slow down e-mail programs
  15. Regular updates help fight spam as new types appear

Requirements:

  • Apple Mail or Microsoft Entourage (X, 2004 or 2008) e-mail program
  • PowerPC or Intel Mac
  • Mac OS X 10.4 or higher, or Mac OS X Server 10.4 or higher
  • 10 MB free hard disk space
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Added: 2009-08-24 License: update/patch Price: Notavailable
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JGuiB 3.0

JGuiB 3.0


JGuiB - Java GUI for Boomer more>>
JGuiB for MacOS X is a GUI written in Java (JDK v5.0) which has been designed and implemented to work with Boomer which is an excellent PK/PD modeling program.

JGuiB turns interactive mode of Boomer into a GUI-based (window) application using command-line mode of Boomer. JGuiB includes three most commonly used functions of Boomer in PK/PD modeling: normal fitting, simulation and Bayesian estimation.

JGuiB is able to process more than one PK/PD model (max. 4 models in one project file) with various weighting schemes simultaneously using one data set. Meanwhile, Bayesian estimation can also be applied to the field of clinical pharmacokinetic services with only one single data point Cp at steady-state.

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Added: 2007-06-29 License: Freeware Price:
847 downloads
newLISP 10.1.6

newLISP 10.1.6


newLISP is a brilliant and simple to use Lisp-like, general-purpose scripting language more>> newLISP 10.1.6 is a brilliant and simple to use Lisp-like, general-purpose scripting language. It has all the magic of traditional Lisp but is easier to learn and use. newLISP is friendly, fast, and small. Most of the functions you will ever need are already built in. newLISP runs on most OS platforms.

Major Features:
  1. A Modern Built-In API
    • Indexing into nested lists and implicit indexing
    • Nested associations
    • Regular expressions PCRE
    • Pattern matching with match and unify
    • Networking functions: TCP/IP, UDP, HTTP, ICMP
    • XML functions
    • Advanced Math and classic Statistics functions
    • Bayesian Statistics functions
    • Financial functions
    • Date and time functions
    • I/O transparent over local files or remote files via HTTP
    • Name spaces (contexts) for programming in modules
    • FOOP Functional Object Oriented Programming. See example new
    • Distributed computing support with remote evaluation and HTTP file API.
    • Cilk-style API for multiprocessor support new
  2. Expandable API
    • import functions from C libraries
    • Modules for MySQL, SQLite, Zlib, Crypto, Postscript etc.
    • document generation support for user written modules: newLISPdoc
  3. Complete Documentation
    • Users Manual and Reference
    • Cookbook for common solutions Code Patterns in newLISP
    • Introductions, e.g.: Introduction to newLISP
    • Training videos; see Documentation page
  4. Advanced Automatic Memory Management
    • ORO memory management
    • Synchronous for repeatable processing times in real-time tasks
    • Fast and lower on resources
  5. Multiprocessing
    • UNIX forks (not on Win32)
    • Semaphores
    • Shared memory
    • local domain UNIX sockets for fast IPC (not on Win32)
    • Cilk-style multiprocessing API
    • Since v.10.1 a messaging API for process inter communication
  6. Distributed Computing Support
    • net-eval function for remote evaluation on multiple network nodes
    • HTTP and net-eval server modes built-in (no code required)
    • most file operations can take URLs
  7. 64-bit support
    • 64-bit standard for integers and some file operations in the standard 32-bit versions
    • LP64 Memory model support makefiles for LINUX, MacOS X and SOLARIS, TRU64
  8. Small and portable
    • Only around 200KB in size (depending on platform and compile flavor)
    • Very fast load time for CGI and scripts
    • Uses only very essential UNIX libs found on the smallest systems
    • Makefiles for FreeBSD, NetBSD, OpenBSD, Mac OS X, LINUX, SOLARIS, TRU64, Win32.
  9. Embeddable
    • Shared library versions for all Platforms (.so, .dylib, .dll)
  10. International
    • UTF-8 and Unicode support compile flavors
  11. Enterprise
    • fully documented
    • support via responsive community
    • Modules in isolated namespaces
    • Automatic generation of source code API documentation using newLISPdoc utility (similar to javadoc).
Enhancements:
  • New and changed functionality: New reader-event specifies an event handler to translate expressions as they are read by newLISP when loading source. This can be used to create a reader, rewrite macro facility
  • Changes and additions in external files:
    • The SQLite sqlite3.lsp module has been expanded with parameter binding fucntionality for safer ussage of the database in web applications, where the danger of SQL injection exists. Bug fixes
    • The new module macro.lsp implements a rewrite macro facility
  • Bug fixes:
    • The inf return value in floating point opertions is now signed (v.10.1.6): (div -1 0) ? -inf
    • mod now returns NaN when the divisor (second argument) is 0 (v.10.1.6): (mod 10 0) ? NaN
    • Memory was not freed correctly when using starts-with/ends-with with regular expressions
    • Under some circumstances nil and true could confuse the sort and unique functions


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Added: 2009-10-22 License: GPL Price: FREE
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Other version of newLISP
newLISP 10.0.8Bayesian Statistics functions. Financial functions. Date and time functions. Distributed applications support. I/O transparent over local files or remote files via HTTP. Expandable API: Import
Price: FREE
License:GPL
Download (949KB)
11 downloads
Added: 2009-06-13
Crux 1.0.0

Crux 1.0.0


A free software toolkit for molecular phylogenetic inference that runs on (at least) Mac OS X, Linux, FreeBSD more>> A free software toolkit for molecular phylogenetic inference that runs on (at least) Mac OS X, Linux, FreeBSD

Crux is structured as a set of Python modules, which makes it possible to quickly develop Python scripts that perform unique, non-canned analyses.
The Python language is elegant and powerful, but it does not have any high performance implementations, which does make it a challenge to use for scientific computing.
Crux is actually implemented as a combination of Python, Cython and C code. Cython is a superset of Python, with various features that allow compiled results to substantially out-perform pure Python code.
The result is that Crux supports a wide variety of users:
- End users can use canned scripts, either those included with Crux, or scripts developed for them by computer-savvy collaborators.
- Computer-savvy users can develop custom scripts that utilize the components of Crux in unforseen ways.
- Power users can use Crux as a component of a custom software package, or extend Crux itself. The source code is available under a very permissive license, with the intent that it be used.

Main features:
- Multifurcating trees can be manipulated at a low level. Various standard operations are implemented, such as canonization (ordering the tree according to a ranking of the taxa), collapsing of zero-length branches, Robinson-Foulds distance computation, and so on.
- Parsers are included for various file formats, including Newick trees, FASTA sequences, and PHYLIP distance matrices.
- Pairwise distances between sequences can be computed based on percent identity, or using methods that correct for multiple hits (Jukes-Cantor, Kimura, and logDet).
- The neighbor joining (NJ) and relaxed neighbor joining (RNJ) implementations are among the fastest in existence, along with Clearcut.
- Tree log-likelihoods can be computed under a variety of models, including all specializations of GTR+I+? and mixture models. Tree likelihoods can be computed in parallel via pthreads. Additionally, Crux is capable of simulating character data under any model its likelihood engine is capable of. The huge range of simulation options makes a canned command line interface like that of Seq-Gen rather unweildy, so simulation is perhaps the most obvious compelling reason to develop Crux scripts.
- Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis coupling and optional MPI support for parallel computation) can sample among non-nested models using reversible model jumps. Polytomous trees can be sampled, also via reversible jumps. In fact, every model parameter that Cruxs MCMC implementation estimates can be expunged via reversible jumps.

System requirements:
- Xcode (to build Crux from source)

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Added: 2009-06-06 License: Freeware Price: FREE
3779 downloads
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