Scaffold Hunter v2.6.0 has been published today. This release primarily contains improvement "under the hood". We have updated the cheminformatics library "Chemisty Development Kit" (CDK), which is heavily used for various tasks by Scaffold Hunter, to its latest version. With this update we are able to deliver isotope and stereochemistry support, a fresh SVG generator for the molecular depiction, faster and more robust dataset imports, and fixes for many long-standing bugs. ... read more
Scaffold Hunter v2.5.1 has been published today. This is a bugfix and performance release and should be a pleasant and safe update for every user of Scaffold Hunter 2.5.0.
Among the optimizations are Cloud View memory usage reduction, parallel distance matrix initialization and the ability to cluster more than 65536 molecules with exact SAHN clustering algorithms.
For more detailed information see the changelog  or the Git history . You can download the latest version from https://sourceforge.net/projects/scaffoldhunter/files/2.5.1/... read more
Scaffold Hunter v2.5.0 has been published today. This release adds a new cloud view  and includes design, work flow, and stability improvements.
The cloud view  displays the scaffold nodes of a subset in a way that is typically used by the popular word clouds. It allows to view small subsets in a compact and intuitive way. Furthermore, it supports quick filtering, property to color mapping and scaffolds frequency highlighting. The cloud view was developed during the Google Summer of Code 2014 by Andrew Zhilka.... read more
Development of Scaffold Hunter advances and so are the tools we are using. To serve a modern version control system for our contributors, we have moved from SVN to Git today. You can find our new repository here .
A hotfix release for Scaffold Hunter has been published today. It fixes a bug, which causes the new heat map view to use 100% of one CPU core, whenever the view is active. Furthermore, this release enhances the heat map view with small workflow changes, such as an automatic sizing of the dendrogram, property and heatmap part.
For more detailed information see the changelog  or the SVN history . You can download the latest version from https://sourceforge.net/projects/scaffoldhunter/files/2.4.1/... read more
Scaffold Hunter v2.4.0 has been published today. This release adds a new heat map view  and includes many design, work flow, and stability improvements. Starting with this release, we officially support MariaDB as a MySQL alternative.
The heat map view  displays hierarchical clustering results in a new way. It visualizes the property values by colors in a 2D matrix of molecules vs. properties. Similar molecules and similar properties are grouped together with the help of clustering, such that molecular similarities which are correlated to property similarities can be easily identified by visual inspection. The heat map view was developed during the Google Summer of Code 2014 by Werner Sturm.... read more
This release contains several bugfixes and minor improvements. It includes an revised color legend used for property mapping in all views and unified keyboard shortcuts. For more detailed information see the changelog  or the SVN history . You can download the latest version from https://sourceforge.net/projects/scaffoldhunter/files/2.3.2/
This year, we had three students working on projects during Google Summer of Code 2014. All have been successful and passed the final evaluation.
Andrey Zhylka was working on the project "Molecule Clouds", a rummage table for scaffolds. Werner Sturm was working on "Heatmaps and Dendrograms", an intuitive visualization for hierarchical clusterings. Last but not least Shamshad Alam added a command line interface to Scaffold Hunter, which is able to cover the major data processing tasks without starting the GUI. ... read more
This release introduces several small features and includes many bugfixes, usability improvements and performance optimizations with the goal to support larger datasets. The added features include new options to create subsets and to export images from the TreeMap view. These features were implemented by Shamshad Alam and Andrew Zhilka who both participate in this year's Google Summer of Code. Thanks for contributing to Scaffold Hunter!
The bugs fixed are mostly related to property mapping and the layout of GUI elements. For more detailed information see the changelog  or the SVN history . You can download the latest version from https://sourceforge.net/projects/scaffoldhunter/files/2.3.1/... read more
Good news for Scaffold Hunter: We were accepted for Google Summer of
Code (GSoC) again this year. Many thanks to Google!
This is a good opportunity to improve the tool further and mentor students that are
interested in our projects:
There might be inquiries and proposals on this and other mailinglists
for some time now.
We will start most of the discussion on Scaffoldhunter-users, and move
more detailed stuff to Scaffoldhunter-develop or switch to off-list
emails with interested students later.... read more
Scaffold Hunter v2.3.0 has been published today. This release does a huge step forward in functionality and stability. It adds a new tree map view and includes many small design and work flow improvements, and even more bug fixes.
The tree map view displays the scaffold tree in a new way, that is especially suited for large data sets and subtree comparisons (see screenshot ). It was developed during the Google Summer of Code 2013 by Jeroen Lappenschaar. ... read more
We had two students working on projects during this year's Google Summer of Code, and both
have been successful and have passed the final evaluation.
Jeroen Lappenschar was working on Ramachandran Plots, Treemaps, and Heatmaps, adding new ways to
visualize data. Falk Nette was working on Image Visual Feature Selection, adapting Scaffold
Hunter for use in medical image retrieval.
We would like to congratulate Jeroen and Falk on their success and thank them for their effort and
enthusiastic work. The results improve Scaffold Hunter by additional features and new graphical
data representations. ... read more
There is a new publication on Scaffold Hunter, published in the journal
The article "Visual Analysis of Biological Activity Data with Scaffold Hunter"
contains a exemplary workflow for the analysis of biological activity data
and describes the main features of Scaffold Hunter.
A best software prize was awarded to Scaffold Hunter at the OpenTox Euro 2013 InterAction Meeting in Mainz. We were very pleased to have the opportunity to present Scaffold Hunter at the workshop!
We have created a tutorial, which will guide you through the first steps using Scaffold Hunter. The document explains the installation and data import process in detail. The individual views and basic concepts of the tool are demonstrated using a sample dataset. We hope that the tutorial helps you getting started with Scaffold Hunter!
Scaffold Hunter v2.2.0 has been published today. This release features a new selection browser, which allows you to easily locate selected molecules in different views, and includes several bug fixes and minor improvements. For more information see the changelog or the SVN history.
You can download the latest version from https://sourceforge.net/projects/scaffoldhunter/files/2.2.0/
We have added a sample data set and a short guide to help you to try out Scaffold Hunter and to get started quickly.
The data set is available for download from https://sourceforge.net/projects/scaffoldhunter/files/datasets/
Good news for Scaffold Hunter: We were accepted for Google Summer of Code (GSoC) after our first application for participation this year.
This is exciting and a good opportunity to spread the word about Scaffold Hunter, get things done, and mentor students that are interested in our projects:
There might be inquiries and proposals on email@example.com and other mailinglists for some time now.... read more
Scaffold Hunter v2.1.3 has been published today. This release fixes bugs related to data import and clustering and includes an improved manual. For more information see the changelog or the SVN history. You can download the latest version from https://sourceforge.net/projects/scaffoldhunter/files/2.1.3/
Scaffold Hunter v2.1.2 has been published today. This release fixes several bugs as well as minor flaws related to the GUI. For more information see the changelog or the SVN history. You can download the latest version from https://sourceforge.net/projects/scaffoldhunter/files/2.1.2/
Scaffold Hunter v2.1.1 has been published today. This is basically a bugfix release and it introduces no new features. Scaffold Hunter is now considered compatible with Java 7. Therefore it should be a pleasant update for everyone using v2.1.0. For more information see the changelog or the SVN history. You can download the latest version from https://sourceforge.net/projects/scaffoldhunter/files/2.1.1/
Scaffold Hunter v2.1.0 has been published today. The release features a new heuristic SAHN clustering algorithm designed for large datasets as well as various minor improvements and bugfixes. You can download the latest version from https://sourceforge.net/projects/scaffoldhunter/files/2.1.0/
Please note that this release breaks compatibility with sessions created by previous versions of Scaffold Hunter. Old sessions can not be resumed!
The Scaffold Hunter website http://scaffoldhunter.sourceforge.net has been revised to provide up to date information on the latest release. Starting from now, all news regarding Scaffold Hunter will be posted here at our Sourceforge project site. This allows you to stay up to date, e.g., using the following RSS feed: https://sourceforge.net/export/rss2_projnews.php?group_id=261360
A release candidate for Scaffold Hunter v2 has been published today.
Lots of new features are added, including new views (plot, dendrogram, and table view), clustering algorithms, a sophisticated graphical data import interface for data integration, and improved data and session management.
You can find the RC using the "Files" facility at the project web page
The first stable version of Scaffold Hunter was released today on SourceForge following publication on the Nature Chemical Biology website.
Scaffold Hunter is a tool for visualization of and navigation through chemical space in an easy, intuitive way. It enables scientists like chemists or biologists to mine their structure-related data and to generate ideas about future research directions.
The tool and its application are describe in the current issue of Nature Chemical Biology (http://www.nature.com/nchembio/journal/v5/n8/full/nchembio.187.html).
The underlying scaffold tree databases are generated with SaffoldTreeGenerator, which is also available from the same project.