dataset
Madagascar 0.9.8
Software package for geophysical data processing and reproducible numerical experiments Madagascar is an open-source software package for multidimensional data analysis and reproducible computational more>> Software package for geophysical data processing and reproducible numerical experiments
Madagascar is an open-source software package for multidimensional data analysis and reproducible computational experiments.
Madagascar aims to provide:
- a convenient and powerful environment
- a convenient technology transfer tool
for researchers working with digital image and data processing in geophysics and related fields. Technology developed using the Madagascar project management system is transferred in the form of recorded processing histories, which become "computational recipes" to be verified, exchanged, and modified by users of the system.
Main features:
- Madagascar is a modern package. Started in 2003, and publicly released in 2006 it was developed entirely from scratch. Being a relatively new package, it follows modern software engineering practices such as module encapsulation and test-driven development. A rapid development of a project of this scope (more than 300 main programs and more than 3,000 tests) would not be possible without standing on the shoulders of giants and learning from the 30 years of previous experience in open packages such as SEPlib and Seismic Unix. We have borrowed and reimplemented functionality and ideas from these other packages.
- Madagascar is a test-driven package. Test-driven development is not only an agile software programming practice but also a way of bringing scientific foundation to geophysical research that involves numerical experiments. Bringing reproducibility and peer review, the backbone of any real science, to the field of computational geophysics is the main motivation for Madagascar development. The package consists of two levels: low-level main programs (typically developed in the C programming language and working as data filters) and high-level processing flows (described with the help of the Python programming language) that combine main programs and completely document data processing histories for testing and reproducibility. Experience shows that high-level programming is easily mastered even by beginning students that have no previous programming experience.
- Madagascar is an open-source package. It is distributed under the standard GPL open-source license, which places no restriction on the usage and modification of the code. Moreover, access to modifying the source repository is not controlled by one organization but shared equally among different developers. This enables an open collaboration among different groups spread all over the world, in the true spirit of the open source movement.
- Madagascar uses a simple, flexible, and universal data format that can handle very large datasets but is not tied specifically to seismic data or data of any other particular kind. This "regularly sampled" format is borrowed from the traditional SEPlib. A universal data format allows us to share general-purpose data processing tools with scientists from other disciplines such as petroleum engineers working on large-scale reservoir simulations.
System requirements:
-
Enhancements
- New reproducible papers, several structural changes, and numerous bug fixes.
Fast Data Transfer 0.8.0
Fast Data Transfer - Efficient Data Transfers capable of reading and writing at disk speed over wide area networks more>>
FDT is based on an asynchronous, flexible multithreaded system and is using the capabilities of the Java NIO libraries.
FDT may be used to stream a large set of files across the network, so that a large dataset composed of thousands of files can be sent or received at full speed, without the network transfer restarting between files.
Main features:
- Streams a dataset (list of files) continuously, using a managed pool of buffers through one or more TCP sockets.
- Uses independent threads to read and write on each physical device
- Transfers data in parallel on multiple TCP streams, when necessary
- Uses appropriate-sized buffers for disk I/O and for the network
- Restores the files from buffers asynchronously
- Resumes a file transfer session without loss, when needed
ParaView 3.4
ParaView offers users a versatile, professional data analysis and visualization application. more>> ParaView 3.4 offers users a versatile, professional data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaViews batch processing capabilities.
ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.
DSpace 1.5.1
Capture, store, index, preserve and redistribute an organizations research material in digital formats more>> Capture, store, index, preserve and redistribute an organizations research material in digital formats
DSpace is a groundbreaking digital repository system, that captures, stores, indexes, preserves and redistributes an organizations research material in digital formats.
Research institutions worldwide use DSpace for a variety of digital archiving needs - from institutional repositories (IRs) to learning object repositories or electronic records management, and more.
DSpace accepts all manner of digital formats. Some examples of items that DSpace can accommodate are:
- Documents, such as articles, preprints, working papers, technical reports, conference papers
- Books
- Theses
- Data sets
- Computer programs
- Visualizations, simulations, and other models
- Multimedia publications
- Administrative records
- Published books
- Overlay journals
- Bibliographic datasets
- Images
- Audio files
- Video files
- eformatted digital library collections
- Learning objects
- Web pages
NOTE: DSpace is distributed and licensed under the terms of the BSD License.
Enhancements:
- (Scott Phillips) Fixed bug where users could not finish registering nor reset their password because the authentication method signatures were changed.
- Jay Paz (SF#1898241) Additional fixes to patch to enable reuse of methods.
- Added the ability to manage sessions with site wide alerts to prevent users from authenticating.
- Fixes a bug where the ability to edit an item durring workflow step 2 is not displayed.
- Jay Paz (SF#1898241) Add item Export from jspui and xmlui.
- Added easy support for google analytics statistics
- Added the ability for super admins to login as other users.
- Added an activity viewer to the Control Panel
- Fix for SF Bug #2082236 Subscription notification (sub-daily) no emails sent
- [2102580] William Hays: Duplicate Handle exception when replacing bitstreams
- [2102617] Sands Fish: X509Authentication fails to assign appropriate specialgroups
- (Sands Fish) Add "Select Primary Bitstream" functionality to submission workflow
- Guard against Community/Collection metadata having only whitespace characters and eliminate cases where null pointer exceptions would be thrown
- Improve DSIndexer logic in both branches to support removal of items from index when withdrawn from repository.
- (Sands Fish) Provides fix for AuthenticationUtil where users IDs are not properly compared.
- Fix NullPointerException cause by nullified Context object in LNI map item to new collection.
- Block Basic Authentication "details" from being exposed in dspace logs.
- (Bill Hays) Close InputStreamReaders explicitly to release any file handles back to OS.
- correct linking on pages when xmlui is the ROOT webapplication
- correct issue with sitemap redirection of mydspace uri.
- Add serlet-api to overlay wars to reduce compile time errors when adding classes
- Correct issues in feed generation
- XMLUI Adjust Advanced Search to use search properties from dspace.cfg.
- Correct bug in Body.toSAX where startElement is called instead of end element.
- Correct issue with libraries being excluded from wars
- Fix for SF bug #2090761 Statistics wrong use of dspace.dir for log location
- Fix for SF bug #2081930 xmlui hardcoded strings in EditGroupForm.java
- Fix for SF bug #2080319 jspui hardcoded strings in browse
- Fix for SF bug #2078305 xmlui hardcoded strings used in UI in xmlui-api
- Fix for SF bug #2078324 xmlui hardcoded strings used in UI in General-Handler.xsl
- SF patch #2076066 Review in jspui submission non-dc metadata
- SF Bug #1983859 added Foreign Lucene Analyzers to poms
- SF Bug #1989916: missing LDAP authentication key
- [1947036] Patch for SF Bug1896960 SWORD authentication and LDAP + [1989874] LDAPAuthentication
- pluggable method broken for current users
- Added copying of registration email template to 1.4 to 1.5 upgrade instructions
- Fix for SF bug #2055941 LDAP authentication fails for new users in SWORD and Manakin
- [1990660] SWORD Service Document are malformed / Corrected Atom publishing MIME types
- Updated installation and configuration documents for new statistics script, and removed references to Perl
- Fix for SF bug #2095402: Non-interactive Submission Steps dont work in JSPUI 1.5
- Fix for SF bug #2013921: Movement in Submission Workflow Causes Skipped Steps
- Fix for SF bug #2015988: Configurable Submission bug in SubmissionController
- Fix for SF bug #2034372: Resorting Search Results in JSPUI always gives no results
- Updates to Community/Collection Item Counts (i.e. strengths) for XMLUI.
- 1.5 upgrade instructions were missing Metadata Registry updates necessary to support SWORD.
- Fix various problems with resources potentially not being freed, and other minor fixes suggested by FindBugs
- Replace URLEncoder with StringEscapeUtils for better fix of escaping the hidden query field
- Fix #2034372: Resorting in JSPUI gives no results
- Fix #1714851: set eperson.subscription.onlynew in dspace.cfg to only include items that are new to the repository
- Fix issue where the browse and search indexes will not be updated correctly if you move an Item
- Fix problem with SWORD not accepting multiple concurrent submissions
- Fix #1963060 Authors listed in reverse order
- Fix #1970852: XMLUI: Browse by Issue Date "Type in Year" doesnt work
- Statistics viewer for XMLUI, based on existing DStat. Note that this generates the view from the analysis files (.dat), does not require HTML report generation.
- Fixed incorrect downloading of bitstream on withdrawn item
- Add JSPUI compatible log messages to XMLUI transformers
- Clean up use of ThreadLocal
- Improved cleanup of database resources when web application is unloaded
- Fix bug #1931799: duplicate "FROM metadatavalue"
- Fixed Oracle bugs with ILIKE operators and LIMIT/OFFSET clauses
Statist 1.0.1
Statist - Statistics program more>>
Enhancements:
- binaries for MacOSX (2 version: one with english, and one with german user feedback in the shell/terminal).
ConverTable Planets 1.7
ConverTable Planets - Teaching tool for unit conversions and gravity more>>
Main features:
- Find out how much you would weigh on the Moon, Mars, and 24 other places in the solar system.
- View the planets and included moons in their true relative sizes!
- Learn how many Venusian (or Martian, Saturnian, etc.) years old you are!
- Planets included (the whole solar system, of course!): Mercury, Venus, Earth, Mars, Jupiter, Saturn, Uranus, Neptune, and Pluto.
- Moons included: Earths Moon, Io, Europa, Ganymede, Callisto, Mimas, Enceladus, Tethys, Dione, Rhea, Titan, Iapetus, Miranda, Umbriel, Titania, Oberon, Triton, and Charon.
- Several mass and weight units are available: kilograms, pounds, grams, milligrams, stones, troy ounces, slugs, newtons, metric tons, and metric carats.
- Brief discussion of the common "mass or weight" language confusion, and what exactly is a "year."
- French localized version available.
Enhancements:
- added "Year Conversions" function to compare year (orbital period) lengths on the planets.
- improved some planet and moon descriptions
- added planet and moon datasets which appear in the "Year Conversions" section
- changed to a primarily single-window interface.
ConverTable Planets X 1.7
ConverTable Planets X is such a program which works great and has a friendly interface. more>>
Enhancements:
- Adds "Year Conversions" to compare lengths of years on various planets
- New planetary dataset display
- Expanded planet and moon descriptions
- Now primarily uses a single-window interface.
Distillation Designer v1.0.4
Distillation Designer brings users a simple McCabe-Thiele method for designing binary distillation systems. more>>
Distillation Designer v1.0.4 brings users a simple McCabe-Thiele method for designing binary distillation systems. It will be of use to students studying Chemical Engineering and is currently being offered as 'donation ware'.
Major Features:
- Boiling Point Graph showing Vapour-Liquid Compositions.
- q-Line calculation from component thermodynamic properties.
- Manually defining the minimum reflux ratio.
- Loading of Data files.
- Plot of Reflux versus stages to help determine the optimal value.
- Drag and Drop graphs direct to desktop.
- Configurable printing of the 3 Graphs
- Much better checking of input data before the McCabe-Thiele graph can be plotted.
- Very basic help.
Enhancements:
- Improved handling of data files.
- Fixed dataset problem when loading an existing design
- Fixed rendering VLE diagram for some composition types.
- Apple Macintosh running Mac OS 10.5 (Intel and PowerPC).
ERDDAP 1.18
Scientific application that refers mostly to oceanographic data more>> Scientific application that refers mostly to oceanographic data
ERDDAP (the Environmental Research Divisions Data Access Program) aggregates scientific data from diverse local and remote sources and offers a simple, consistent way to download subsets of the data in common file formats and make graphs and maps.
This particular ERDDAP installation has oceanographic data (for example, data from satellites and buoys).
Without ERDDAP, when a person (or a computer program) looks on the Internet for a specific type of scientific data (for example, oceanographic data like satellite sea surface temperature data), there are many problems.
Main features:
- Aggregates data from diverse local and remote sources.
- Offers several ways to search for datasets of interest (see options at right).
- Lets you make requests in a standardized way, regardless of the data sources request protocol.
- Gridded data is available via the DAP hyperslab protocol and WMS.
- Tabular data is available via the DAP constraint protocol.
- ERDDAP also provides Data Access Forms (web pages) which help humans create the DAP requests. OPeNDAPs DAP is the recommended IOOS DMAC data transport mechanism and a NASA EOSDIS standard. (DAP is great!)
- lets you choose the file format for the results (for example, .html table, ESRI .asc, Google Earth .kml, .mat, .nc, .csv, .tsv, .json, .xhtml, .png).
standardizes the dates+times in the results, either as:
- To avoid time zone and daylight savings confusion, time values are always converted to the UTC time zone.
lets you request .png and .pdf image files with graphs and maps of the data, in addition to the raw data. Three special uses of these images are:
- Web page authors can embed a graph with the latest data in a web page using an HTML tag.
- Anyone can use ERDDAPs Slide Sorter to build a personal web page that displays graphs with the latest data (or other images or HTML content), each in its own, draggable slide.
- Anyone can use or make Google Gadgets to display images with the latest data on their iGoogle home page.
- Offers email/URL and RSS subscriptions, so you can be notified whenever a dataset changes.
- Is a web application (for humans with browsers) and a web service (for computer programs). ERDDAP has REST- and ROA-style links to make ERDDAPs services available to computer programs, so that other web applications and web services can be built on top of ERDDAP.
Jailer 2.9.10 Beta / 2.9.9
Open source mass data export to XML and SQL more>> Open source mass data export to XML and SQL
Jailer is a tool for database subsetting and sampling, schema browsing, and rendering. Jailer exports consistent, referentially intact row-sets from relational databases.
Jailer removes obsolete data without violating integrity. Jailer is DBMS agnostic (by using JDBC), platform independent, and generates DbUnit datasets, topologically sorted SQL-DML, and hierarchically structured XML,
NOTE: Jailer is licensed and distributed under the Apache License Version 2.0.
Main features:
- Exports consistent and referentially intact row-sets from your productive database and imports the data into your development and test environment.
- Improves database performance by removing and archiving obsolete data without violating integrity.
- Generates hierarchically structured XML, topologically sorted SQL-DML and DbUnit datasets.
- Open Source. Entirely written in Java. Platform independent. DBMS agnostic.
System requirements:
-
- JDBC-driver for your R-DBMS
Enhancements
- fixed a bug concerning multi-line CLOB content.
using JDBC), platform independent, and generates DbUnit datasets, topologically sorted SQL-DML, and hierarchically structured XML, NOTE: Jailer is licensed and distributed under the ApacheLicense:Freeware
Pound-Shell 0.8.6 Alpha
Pound-Shell 0.8.6 Alpha is yet another extremely useful utility designed to act as an automated lab-book for people that conduct experiments in their standard shell environments more>>
Pound-Shell 0.8.6 Alpha is yet another extremely useful utility designed to act as an automated lab-book for people that conduct experiments in their standard shell environments. The high-level goal of Pound-Shell is to allow users to log data processing experiments (with little/no manual effort or interference) in such a way that they can later go back and recall (or rediscover) and reproduce their steps.
Basically, it's designed to help us determine data's provenance. Further, Pound-Shell allows users to almost automatically re-run old experiments with new data. This type of work includes processing files with R, using gnuplot, interactive perl/python, standard data processing with shell commands (awk, sort, join, etc.), etc. Pound-Shell does not attempt to trace commands if it detects that a program has "captured the screen". Examples include Vim, emacs, etc. In such cases, Pound-Shell waits for the sub-process to end and then resumes recording.
With Pound-Shell, you can send a colleague your data-set(s) and your lbsh lab-book, and they can understand/reproduce/verify your results with Pound-Shell's automated tools. In essence, you simply run "lbsh" and it automatically creates a new shell (the same type [bash | tcsh | etc.] that you already use) in a child process. Figure 1 shows how your session goes through Pound-Shell to the real shell underneath.
When you decide you want to start logging commands for an experiment, you tell Pound-Shell to start logging. Then Pound-Shell simply records your commands (and also traces into the above mentioned tools). It does not record passwords, or anything else that is not output the screen. You can use tab-completes, issue commands that span multiple lines, use shell history, etc. When you are done, you tell Pound-Shell to stop logging. Then you may do whatever and Pound-Shell will quietly wait. You may repeat as needed without having to restart Pound-Shell each time.
Major Features:
- It is able to provide its utility without requiring the user to behave any differently. In a sense, users are free from needing to learn the diligence practiced by other scientists in their labs. In other words, it should make people's lives easy w/o being painful.
- It has processing scripts (file-provenance.pl, exeggutor.pl, etc.) that allow one to specify a file name (such as a graph) and see all of the experiments that were needed to derive its data. The history (or provenance) of files can be seen as an ordered list of experiment IDs or as a Dataset Derivation Graph (or DDG).
- It can be used to re-run experiments with new or old data to update findings or reproduce prior results using a file's provenance.
Enhancements: Jun 11 2008
- Fixed bug: Ctrl-d is not captured, so if it is used to exit a process like gnuplot or python, it will not make it to the script.out file
Mapyrus 0.807
A software to plot Geographic Information System data to PostScript more>> A software to plot Geographic Information System data to PostScript
Mapyrus is a software to plot Geographic Information System data to PostScript, PDF, SVG and web image files. Mapyrus combines a BASIC-like scripting language, reading GIS datasets and running as either a utility program, a Java Servlet, or as a webserver.
Main features:
- Graphical output to web-image, PostScript, Portable Document Format (PDF) and Scalable Vector Graphics (SVG) formats.
- Display of lines, polygons and other shapes including options for fancy linestyles, hatching, gradient fill and other patterns.
- Transparent colors. Colors defined by name, RGB values or Hue-Saturation-Brightness.
- Optional anti-aliasing of lines and labels.
- Clip polygons.
- Display of labels, including tabular display and user-defined fonts.
- Display of images, including geo-referenced images.
- Running as a stand-alone utility program, or as a self-contained web server.
- Use of geometrical algorithms from Java Topology Suite library.
System requirements:
-
Enhancements
- Add AXIS function to generate suitable values for a graph axis.
- Add CROSSES function from Java Topology Suite.
- Add ++ and -- for incrementing and decrementing variable values.
- Add ability to run as a servlet.
SphinxReport 1.0 Alpha 3
A report generator written in python using sphinx and matplotlib more>>
Once the pipeline settles down, SphinxReport permits an easy transition towards the automatic report generation needed when the pipeline is run on new data sets. SphinxReport is easy to use and powerful enough to give all the flexibility needed during the development of computational pipelines and robustness during the production use of a pipeline. It is intended for developers and computational scientists with python scripting experience.
Major Features:
- Uses simple markup in the form of restructured text
- Supports both automated and narrative analysis
- Keeps code, data and text together
- Takes care of indexing and formatting to produce something presentable
- Produces static html, latex, ps and pdf.
Limbas 1.12.115
A web-based enterprise software factory. LIMBAS is a web-based enterprise software factory. Thanks to LIMBASs built-in modules (tables/lists, formular, PDF report, groupware, document manager (DMS), more>> A web-based enterprise software factory.
LIMBAS is a web-based enterprise software factory. Thanks to LIMBASs built-in modules (tables/lists, formular, PDF report, groupware, document manager (DMS), workflow) design your ECM, CRM or any intranet solution fitting 100% of your needs.
Enhancements
- table names : rename system tablenames to namespace compatible names
- namespace : support of name/id space for compatibility of limbas solutions
- formular : supports sub tables formular supports tableforms from related sub tables
- file structure : split filestructure to dependend files and independend core
- userrights : for datasets singe user or grouprights can be set for single datasets
- snapshot : validation snapshots now can be validate against changes in databasestructure
- copy/versioning : error in copy or versioning with fields of type upload fixed
- remote import : remote import functionality fixed
- report : select orderstrategy by Z-Index or Y-Position
- report : posibility of transparent background color in Tables
- report : print more as one report in the list
- fieldtypes : local language support for field-types
- file table : new field type "Content Referenz" for systemtable "files"
- secuity : userattribut for use only static ip
- order of fields : wrong oder of fields when owner in multible groups fixed
- index : index check for plausibility of indexed words (needed for ocr text)
- relation search of filecontent : posibility of search in indexed filecontent over tables with linked files
- deleting tablegroups : error by deleting tablegroups fixed
- reminder : error after creating a reminder fixed
- versioning : versioning now supports recursive versioning of relations
- versioning : diff viewer shows changes in relations
- versioning : diff viewer alternative output as pdf
- permissions : changing of parent group in group settings
- remote import : execute failed statements after finish import (needed for foreign keys)
- versioning : modify type of versioning-desription-field
- relations : extended relation view extends with drop and delete extension
- relations : extended filters for relation definitions
- DMS : md5 check for files / dublicate check with md5 values / overview for dublicates
- spoap : file-upload with soap interface
- report : table fieldlist popup now with ajax
- data locking : advanced data locking with ajax and user-overview
- limbas trigger : new triggerengine with merging triggers of subgroups
- table sub groups : support of subgroups for better visualization table structure or applications
- export : advanced export functionalities
- field type float : support for power digits
- logging : change logs can displayed as diff
- delete dataset : extended recursive deletion of n:m relations with referential integrity
FlameRobin 0.9.2
Database administration tool for Firebird DBMS more>> Database administration tool for Firebird DBMS
FlameRobin is a software utility that is: lightweight (small footprint, fast execution), cross-platform (Mac OS X, Linux, Windows, FreeBSD, Solaris), and dependant only on other open source software.
Enhancements
- New features
- Allowed deleting from system tables (ex. to stop queries via MON$STATEMENTS)
- Added support for trusted authentication
- Databases can now be recreated from existing registration info
- Transaction isolation level can now be selected in SQL editor
- Win64 port
- Enhancements and Bug fixes
- Fixed problems with mangled UTF8 identifiers
- Improved autoincrement triggers
- Drop FK only once for self-referencing tables in Rebuild script
- Improved management of passwords in connection dialogs
- Case insensitive DoMaIn keyword detection
- Fixed reported length of char fields in DDL extraction of system tables
- Fixed minor DDL extraction problem with BIGINT and scale
- Search words are now highlighted in advanced metadata search results
- DataGrid: sum of values of selected cells in the grid is shown in status bar
- Data grid cell editor now has a popup menu of a standard edit control
- Data of CHAR type using multibyte character set has correct padding now
- Database file size is now reported correctly for databases over 2GB
- Opening pages in tabs can now be controlled with Shift/Control keys
- Information on database property page is reloaded without reconnecting
- Fixed focus problem with property pages
- Fixed broken descriptions of system table columns in property pages
- Optionally display sources of all triggers on table property page
- Controls are now focused before their popup menus are shown
- Improved usability of menus and commands via keyboard
- SQL Editor: Improved detection of field sizes in resulting dataset
- Fixed statement parsing when SUBSTRING function is present
- Fixed column autocompletion for JOINed tables
- Fixed code completion when tables are listed in SQL89 order
- Fixed crash when opening query window and pressing F5 or F8 at once
- Improved the way views are switched in SQL editor
- Fixed completion under Mac OS X
- Other minor improvements and fixes to SQL editor
- Statement execution time is now displayed with milliseconds precision
- Minimum required version of wxWidgets is now 2.8.
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