Free workbench software for mac

Workbench is a Dashboard widget thatacts as a more or less omnipresent text editor pane.
Often I had the problem I had to copy some text (say out of an exception message or an URL) and just either take a short look at it or mutate it to further use (URLs most often). Changing longer URLs in the addressbar of browser is not that nice and in case of IE 7 its horrible.
So I created this dashboard as kind of workbench where I can quick and easy copy things into from different sources (every source that support copy & paste), redo it in place (changing parameter or target in an URL for example) and reuse it by coping the new text into another app.
Always having to open an editor or switching the tasks would be a solution, but I think this one nicer.
Main features:
- Multiple texts
You can even have multiple texts in one widget and you have next, previous, add and delete button to handle them
- Multiple modes:
You have different modes: small mode, big mode and bar mode. Big mode is the original one, small mode was made for those with a smaller screen or lots of other widgets on Dashboard and the bar mode is the ulitmate space saver. You switch between big and small via the "M"-Button and both look quite identically and behave identically.
Bar mode is slightly different. The bar-mode has no text-pane but still it has the buttons and the name of the actual text youre on. You swith from either of the two other modes via double clicking the black frame into the tab more. When you either double click on the frame or use the "M"-button in bar mode you get back to the mode you have been earlier. Also when you click on "+" to add a new text you automatically switch back to the previous mode.

Enhancements
- completly redone the GUI (the code, not the design)
- bugfix of the JS-part

CLC RNA Workbench 4.2 brings you an easy way to a range of complex algorithms and options. RNA secondary structures can be predicted using state-of-the-art free energy minimization algorithms.

Major Benefits:

• You will have easy access to a large number of integrated research tools:
• • Secondary structure prediction
  • Graphical view and editing of secondary structure
  • Tabular view of structures and energy contributions
  • Symbolic representation in sequence view
• You can make your computer a High Performance Computing center
• • Unleash the hidden powers in your CPU with the Bioinformatics Cell
  • Plug in the Bioinformatics Cube and increase your search speed up to 200 times
  • Your research work will be easy to carry out
  • The program is graphically based, intuitive, and user-friendly
  • Share data with your colleagues using CLC Database Solution
• You will have a bioinformatics solution that continuously evolves
• • The frequent program updates keep you up to date with the latest scientific developments. Your ideas for future improvements will have top priority.
• You can customize your workbench
• You have the possibility to customize your workbench through our Software Developer Kit.

Major Features:

1. Bioinformatics features in CLC RNA Workbench
   • Secondary structure prediction
   • Graphical view and editing of secondary structure
   • Tabular view of structures and energy contributions
   • Symbolic representation in sequence view
2. Pattern search
   • Search for sequence matches
   • Motif search for basic patterns
   • Motif search using regular expressions
   • Motif search with ProSite patterns
   • Pattern discovery (unknown patterns)
   • Project and data management
   • Full integration of data input, data management, calculation results, and data export
   • Detailed history log
   • All types of files can be saved in local projects, and launched from the program
   • Import and export of data in a large number of file formats
   • Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects
3. Other bioinformatics features
   • DNA, RNA and protein sequence editor displaying both linear and circular molecules
   • Multiple alignment of DNA, RNA, and proteins
   • • Two proprietary algorithms
     • ClustalW
     • Muscle
     • T-Coffee
     • MAFFT
     • Kalign
   • Joining multiple alignments into one
   • DNA, RNA, and protein alignment editor
   • Interactive logo graphs along both DNA, RNA and Protein alignments
   • Batch processing of analyses on multiple sequences in one work-step
   • Advanced re-alignment and fix-point alignment option
   • Manual annotation of sequences
   • Dot plot based analyses
   • Local complexity region analyses and complexity plots
   • Gap fraction graphs
   • G/C content analysis and graphs
   • Advanced pairwise comparison
   • Extract annotations
4. Database searches
   • Web based sequence search using BLAST
   • BLAST on local databases
   • Build local BLAST databases
   • GenBank Entrez searches
   • PubMed lookup
   • Web based lookup in UniProt, NCBI, and Google

Enhancements:

• New features:
• • Import list of sequences in csv format: each line in the file represents a sequence with name, optional description, and sequence. Typically useful for importing lists of oligos.
  • Advanced view of elements in a folder including batch editing.
  • Extract sequences improvements
  • You can now drag results from NCBI searches into the view area to open directly (previously you could only drag into a folder to save)
  • "Find" in text view now accepts Enter as command to find the next hit
  • Importing VectorNTI archives previously resulted in a sequence list. Now it imports as single sequences.
  • Export of annotations in GFF format (note that annotations with joined regions are not supported)
• Bug fixes:
• • Fixed tblastn numbering issue
  • Problem rendering scatter plots without lines
  • DNA strider files could loose name upon import
  • Rare misplacement of annotations when editing very large sequences
  • Various bug-fixes

CLC Free Workbench creates a software environment enabling users to make basic bioinformatics analyses and smooth data management, combined with nice graphical viewing and output options.
CLC Free Workbench is a tool that enabling users to make basic bioinformatics analyses by create a software environment.
Main features:
- GenBank searching and viewing (linear and circular views)
- Multiple alignment of DNA, RNA and proteins (2 alignment algorithms)
- Advanced alignment editing and sequence editing
- Joining multiple alignments and multiple sequences into one
- Open reading frame determination
- Translation from DNA to proteins (all genetic translation tables)
- Reports with residue composition, molecular weight and iso electric point (for proteins)
- Neighbor-joining and UPGMA phylogenies
- Interactive restriction site analysis and viewing
- Other reporting facilities
- Import/export to a number of data formats
- Launch of external files
- Detailed History Log
- Batch runs of analyses such as DNA to protein translation.
Enhancements:
- Fixed error in conversion of old sequence data with lowercase characters
- Old data can now be converted through the help menu
- Fixed error when trying to save an element to non-selected location
- A few help updates
- Better license handling on Windows Vista
- Fixed error in alignment editing

CLC Sequence Viewer 6.2 is a freeware that creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options.

Major Benefits:

• You will have easy access to a large number of integrated research tools:
• • Creating and editing alignments
  • Interactive restriction site analysis
  • Phylogenetics
  • Integrated GenBank searches
  • Advanced DNA to Protein translation
• You can get easy access to hardware accelerated database searches
• • Plug in the Bioinformatics Cube and increase your search speed up to 200 times
• Your research work will be easy to carry out
• • The program is graphically based, intuitive, and user-friendly
• You will have a bioinformatics solution that continuously evolves
• • The frequent program updates keep you up to date with the latest scientific developments. Your ideas for future improvements will have top priority.
• You will get superior customer service
• • Free support to all users.
    

Major Features:

1. Bioinformatics features in CLC Sequence Viewer
   • Multiple alignment of DNA, RNA, and proteins
   • • Two proprietary algorithms
     • ClustalW
     • Muscle
     • T-Coffee
     • MAFFT
     • Kalign
   • Consensus sequence determination and management
   • Conservation score along alignments
   • Open reading frame determination
   • Easy access to web-based protein and nucleotide search in GenBank, including download facilities and full graphical overview of sequence annotations of your choice
   • Translation from DNA to proteins (all genetic translation tables)
   • Reports with residue composition, molecular weight and iso electric point (for proteins)
   • Neighbor-joining and UPGMA phylogenies
   • Restriction site analysis and viewing
   • Create reverse complement
   • Shuffle sequence
   • Option of viewing and graphical manipulation of bioinformatics analyses made in commercial workbenches from CLC bio
2. Other features in CLC Sequence Viewer
   • Full integration of data input, data management, calculations results, and data export. This eliminates time spent on manual data transfers between different programs and databases
   • All types of files can be saved in local projects and launched from the program
   • Detailed history log
   • User-friendly graphical tools used in order to find and work with relevant regions of DNA, RNA and protein sequences
   • Text-based sequence view
   • Easy printing of reports and graphics
   • Export of user-defined figures to various graphics file formats
   • Import and export of data in a large number of file formats
   • Option of working with different files and in different file projects at the same time
   • Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects

Enhancemnets:

• New features:
• • Import list of sequences in csv format: each line in the file represents a sequence with name, optional description, and sequence. Typically useful for importing lists of oligos.
  • Advanced view of elements in a folder including batch editing.
  • Extract sequences improvements
  • You can now drag results from NCBI searches into the view area to open directly (previously you could only drag into a folder to save)
  • "Find" in text view now accepts Enter as command to find the next hit
  • Importing VectorNTI archives previously resulted in a sequence list. Now it imports as single sequences.
  • Export of annotations in GFF format (note that annotations with joined regions are not supported)
• Bug fixes:
• • Problem rendering scatter plots without lines
  • DNA strider files could loose name upon import
  • Rare misplacement of annotations when editing very large sequences
  • Various bug-fixes

MonsterMind is nothing more than the usual classic game of the Master Mind.
This is a brand new project: we wish to make compatible with the SDL library our collection of old Amiga Workbench Games.
Main features:
- 100% portable using SDL library,
- localizated (actually english and italian),
- seven colors, picked from a stock of sixteen, to guess in fourteen attempts,
- ability to change the backdrop to satisfy your taste,
- you can modify the sixteen colors too,
- different game level (less colors to guess, less number of attempts...),
- possibility to save and load game status,
- and other things you may communicate to us.

The Eclipse Project is an open source software development project dedicated to providing a robust, full-featured, commercial-quality, industry platform for the development of highly integrated tools.
The mission of the Eclipse Project is to adapt and evolve the eclipse technology to meet the needs of the eclipse tool building community and its users, so that the vision of eclipse as an industry platform is realized.
Eclipse is a kind of universal tool platform - an open extensible IDE for anything and yet nothing in particular.
The real value comes from tool plug-ins that "teach" Eclipse how to work with things - java files, web content, graphics, video - almost anything one can imagine. Eclipse allows tool builders to independently develop tools that integrate with other peoples tools so seamlessly you cant tell where one tool ends and another starts.
Main features:
Workbench
- The term Workbench refers to the desktop development environment. The Workbench aims to achieve seamless tool integration and controlled openness by providing a common paradigm for the creation, management, and navigation of workspace resources.
- Each Workbench window contains one or more perspectives. Perspectives contain views and editors and control what appears in certain menus and tool bars. More than one Workbench window can exist on the desktop at any given time.
Java development
- The JDT project provides the tool plug-ins that implement a Java IDE supporting the development of any Java application, including Eclipse plug-ins. - It adds a Java project nature and Java perspective to the Eclipse Workbench as well as a number of views, editors, wizards, builders, and code merging and refactoring tools. The JDT project allows Eclipse to be a development environment for itself.
Team programming with CVS
- In the Concurrent Versions System (CVS) team programming environment, team members do all of their work in their own Workbenches, isolated from others. Eventually they will want to share their work. They do this via a CVS Repository.
Branches
- CVS uses a branch model to support multiple courses of work that are somewhat isolated from each other but still highly interdependent. Branches are where a development team shares and integrates ongoing work. A branch can be thought of as a shared workspace that is updated by team members as they make changes to the project.
- This model allows individuals to work on a CVS team project, share their work with others as changes are made, and access the work of others as the project evolves. A special branch, referred to as HEAD, represents the main course of work in the repository (HEAD is often referred to as the trunk).
Sharing work
- As team members produce new work, they share this work by committing those changes to the branch. Similarly, when they wish to get the latest available work, they update their local workspaces to the changes on the branch.
- Thus the branch is constantly changing, moving forward as team members submit new work.
- The branch effectively represents the current state of the project. At any point a team member can update their workspaces from the branch and know they are up to date.
Plug-in Development Environment
- The Plug-in Development Environment (PDE) provides a rich set of tools to create, develop, test, debug and deploy Eclipse plug-ins, fragments, features, update sites and RCP products. PDE also provides comprehensive OSGi tooling, which makes it an ideal environment for component programming, not just Eclipse plug-in development.

System requirements:
- Apple Java 2 Platform Standard Edition (J2SE) 5, service release 4 for Tiger

Enhancements
- New update UI - The UI for performing installation and updates is completely new in 3.4. The new UI is accessed using Help > Software Updates.
- Viewing available software - You can now view the software thats available for install or update in multiple ways. The Available Software tab in the Help > Software Updates dialog provides a view menu button that lets you view the software by site, category, or name.
- Markers view - A new Markers view has been added for users who prefer to have their problems, bookmarks and tasks in the same view (i.e., as it was back in the days before Eclipse 3.0). It can be found by selecting Window > Show View > Other > Markers.
- New look for Problems, Bookmarks and Tasks views - The Problems, Bookmarks and Tasks views now have a new look, implementing many long-standing feature requests.
- Many more improvements and changes