Category: Miscellaneous

LEAF GUI 2 – Analyze Macroscopic Structure of Veins in Leaves

LEAF GUI 2

:: DESCRIPTION

LEAF GUI (Leaf Extraction and Analysis Framework Graphical User Interface)is designed for plant biologists and ecologists who wish to analyze the macroscopic structure of veins in leaves. The software allows users to extract descriptive statistics on the dimensions and positions of leaf veins and the areoles they surround by following a series of thresholding, cleaning and segmentation algorithms given images of leaves where veins have been enhanced relative to the background.

::DEVELOPER

LEAF GUI Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Window / Linux / Mac OsX

:: DOWNLOAD

LEAF GUI

:: MORE INFORMATION

Citation

Price, C.A., O. Symonova, Y. Mileyko, T. Hilley and J.S. Weitz
Leaf Extraction and Analysis Framework Graphical User Interface: Segmenting and Analyzing the Structure of Leaf Veins and Areoles.
Plant Physiology, 155 (236-245).

REtools 5.0-101 – Assist in Restriction Enzyme Use

REtools 5.0-101

:: DESCRIPTION

REtools is a user friendly and easily customized program to organize any laboratory enzyme stock, brings a software solution that makes restriction enzyme use and reaction condition determination straightforward and efficient.

The usually unexplored potential of isoschizomers becomes accessible to all, since REtools proposes all possible enzymes similar to the one(s) chosen by the user. Finally, many of the commonly overlooked subtleties of restriction enzyme work, such as methylation requirement, unusual reaction conditions, as well as the number of flanking bases required for cleavage, are automatically provided by REtools.

::DEVELOPER

P. Pognonec

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX

:: DOWNLOAD

REtools for Win ; for Mac ; Manual

:: MORE INFORMATION

Citation:

REtools: A laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance. BMC Bioinformatics 2006 Feb; 7:98

Any comment and/or proposal concerning this application is welcome! Please contact P. Pognonec for additional information.

TaxMan 1.1 – Taxonomy Database Manager

TaxMan 1.1

:: DESCRIPTION

TaxMan (Taxonomy database Manager) is a software package that uses freely available bioinformatics tools to allow rapid assembly, storage and analysis of large aligned DNA and protein sequence datasets for user-defined sets of species and genes. Sequence data are obtained from GenBank format files on the basis of annotation and / or sequence similarity. Consensus sequences are built and aligned automatically, and aligned sequences are stored in a database. By using the stored aligned sequences, large concatenated protein and DNA multiple sequence alignments can be rapidly generated for subsets of the dataset. Trees resulting from phylogenetic analysis can also be stored, and compared with a reference taxonomy.

::DEVELOPER

The Blaxter Lab at The Institute of Evolutionary Biology University of Edinburgh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

TaxMan

:: MORE INFORMATION

Citation:

Martin Jones and Mark Blaxter
TaxMan: a taxonomic database manager
BMC Bioinformatics 2006, 7:536

Handlebar 2.2.2 – Web Based Sample Inventory Manager

Handlebar 2.2.2

:: DESCRIPTION

Handlebar is a web based sample inventory manager, originally designed to meet the needs of researchers in the NERC PG&P research projects, it is now available for wider use. It is simple to use, allows a central database to serve users over multiple sites and permits the administrator to easily define new item templates for different types of sample. Linking between related samples is supported. The system is designed to work with printed barcode labels and functions are provided to print labels with Zebra brand barcode printers using the EPL protocol.

::DEVELOPER

the NEBC and the University of Manchester

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Handlebar

:: MORE INFORMATION

If you are interested in using the software or have any questions please contact the author via helpdesk@nebc.nox.ac.uk

 

SAIL 1.0 – Sample avAILability system

SAIL 1.0

:: DESCRIPTION

SAIL (Sample Availability System) is designed to hold phenotype availability information and meta data about samples,experiments and phenotypes, submitted by data owners or databases that contain actual measurement data. By being geared towards a complexity level that focus on describing data and availability rather than the measurements themselves, SAIL provides a way to browse and summarise complex content across diverse resources. This can be used in many different scenarios from designing new studies, understanding previous studies, and finding data and biomaterial from different cohorts that can be combined in meta-analysis studies. SAIL also contains functionality to annotate collections, with tools to create new vocabularies or use terms from standard sample ontologies, and to combine and harmonise vocabularies. The system can handle real valued data as well as availability data, which is useful to match study samples from different cohorts and to find the availability of samples in certain ranges of study parameters or measurements. The SAIL system is an easy and flexible tool for researchers and co-ordinators of sample collections to browse, understand and update large and complex content across many diverse resources to maximize their scientific value and usability.

SAIL Demo

::DEVELOPER

EBI, IMCS and FIMM

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SAIL

:: MORE INFORMATION

SAIL is released under the GNU AFFERO GENERAL PUBLIC LICENSE (AGPL)

Citation:

Mikhail Gostev, etc.SAIL – a software system for sample and phenotype availability across biobanks and cohorts , Bioinformatics (2010)doi: 10.1093

AIMS 2.10 – Assay Information Management System

AIMS 2.10

:: DESCRIPTION

AIMS is a web based system that serves as the central repository for experimental data produced by different experimental technologies (genomic, transcriptomic, proteomic, metabolomic data etc). The basic structure of AIMS resemples that of SIMS, with data organized around three main categories: Studies, Experiments and Assays. However the system is designed to be extremely flexible reagrding its configuration, since it is intended for one instance of AIMS system to be used for data obtained by several different technologies.

::DEVELOPER

EBI, IMCS and FIMM

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

AIMS

:: MORE INFORMATION

Citation:

Krestyaninova M, Zarins A, Viksna J, Kurbatova N, Rucevskis P, Neogi SG, Gostev M, Perheentupa T, Knuuttila J, Barrett A, Lappalainen I, Rung J, Podnieks K, Sarkans U, McCarthy MI, Brazma A. A System for Information Management in BioMedical Studies–SIMBioMS. Bioinformatics. 2009 Oct 15;25(20):2768-9.

 

Trend / jTrend 1.01 – Cellular Automata Simulation Environment

Trend / jTrend 1.01

:: DESCRIPTION

Trend is a general purpose cellular automata simulation environment with an integrated high level language compiler, a beautiful graphical user interface, and a fast, three stage cached simulation engine. This is the simulation system that was used to discover the first emergent self-replicating cellular automata rule set, and the first problem solving self-replication loop.

jTrend is a Java-based cellular automata simulator modeled after Trend. It inherits all the features of Trend such as dynamically changing cellular space sizes and defining the cellular automata rules “on the fly” using the Trend programming language.

::DEVELOPER

Complex Computation Laboratory ,Iowa State University

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /Mac OsX
  • JAVA

:: DOWNLOAD

Registration First ; Trend / jTrend

:: MORE INFORMATION

N/A

SpectFit 2.0 – Non-linear Data Fitting

SpectFit 2.0

:: DESCRIPTION

SpectFit is an interactive non-linear data fitting program.  It is reasonably easy to use and is powerful enough for a wide variety of routine curve fitting.  Strong features are Fourier data analysis, highly versatile fitting methods, and complete documentation.

::DEVELOPER

Steve Andrews

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX

:: DOWNLOAD

SpectFit ; manual

:: MORE INFORMATION

N/A

MICE 1.4 – Mouse Information & Classification Entity

MICE 1.4

:: DESCRIPTION

MICE (Mouse Information and Classification Entity) is a program aimed at facilitating the monitoring of animals in their facility. It consists of a virtual facility in which scientists can perform all the tasks done in the real world (i.e., receiving animals, breeding, etc…). Each animal is recorded with all associated information (birth date, cage number, ID number, tail analysis number, parents, genetic status, genetic background and more), allowing for reliable tracking. Animals can be identified, grouped, sorted, moved…, according to any parameter of interest to the scientist, including associated comments. Crossings are automatically processed by the program, which determines the new genetic background, generation number, cage location and due date.

MICE reminds the user when births are expected, and entering the newborn animals only requires a few clicks (of the mouse!). The genealogy of each animal can be determined in two different ways, including a visual tree from which each ancestor’s information can be retrieved.

::DEVELOPER

P. Pognonec

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX

:: DOWNLOAD

MICE for Win ; for Mac

:: MORE INFORMATION

Citation:

MICE, a program to track and monitor animals in animal facilities. BMC Genetics 2001 Mar;2(1):4

Any comment and/or proposal concerning this application is welcome! Please contact P. Pognonec for additional information.

FCSM – Frozen Cell Stock Monitor

FCSM

:: DESCRIPTION

FCSM (Frozen Cell Stock Monitor) is a virtual nitrogen tank to monitor frozen cell stocks.

FCSM aimed at facilitating the monitoring of biological samples (cell lines, sera, etc) stored in liquid nitrogen containers. It consists of a virtual container in which scientists can “store” their samples and a program recording the location of each sample, cell characteristics, storage dates, names of the manipulators, and much more. Additional comments and a photograph can be associated with each vial, allowing for reliable tracking of samples. Vials can then be identified according to any parameter of interest to the scientist including associated comments. Once identified, the location of these vials is visually presented, simplifying their localization in the real container during retrieval. Thawing of vials is recorded by the program, together with the date and the name of the manipulator.

::DEVELOPER

P. Pognonec

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX

:: DOWNLOAD

FCSM for Win ; for Mac

:: MORE INFORMATION

Citation:

Virtual nitrogen tank to monitor frozen cell stocks. Biotechniques 2000 Jul;29(1):122-6

Any comment and/or proposal concerning this application is welcome! Please contactP. Pognonec for additional information.