DrosophiLab is a freeware program for Microsoft Windows which lets you simulate the genetics of fruit flies, Drosophila melanogaster. You use the supplied Chromosome Editor to create fruit flies with complete control over their genotype. You can then import the flies into the program and derive new generations from them. All individual flies can be examined and rotated in full 3D.
Download Free Drosophila Genetics Lab Program Software
The latest version of the BioTapestry Editor is version 7.1.2, released 9/28/19. Download the copy of BioTapestry that is appropriate for your system. In contrast to previous versions, you no longer need to download and install Java first; these downloads now include the required Java files, and so the program is standalone.
If you need to use an older version of BioTapestry prior to Version 7.1.2, you can still download older versions of the program from the Archived Executables page. Depending on the version and operating system, you may needto install Java as well.
Significant features include:Supporting data resulting from the perturbation of expression of specific genes, measured in any way (QPCR, genetics, etc.), can be easily accessed for each gene or link. Temporal and spatialexpression results are also accessible.
BioTapestry can portray hourly, localized views of the network during development based on data tables describing the network'slocal and temporal states.
BioTapestry can automatically layout the set of network models fromlists of interactions provided either through interactive dialogs or comma-separated value (CSV) files exported by spreadsheet programs.
Running BioTapestry as a Java Web Start application is no longer supported; please use the downloadable versions of the program provided above, whichall include the required Java components needed to run BioTapestry. Our apologies for any inconvenience.
Version 7.1.2 was released on 9/28/19, and the only notable differences from the prior release are that: 1) all platforms bundle therequired Java components; 2) the Windows version is now installed using an install program; and 3) all releases are signed with a current(as of 9/28/19) signing certificate verifying that the software originates from the Institute for Systems Biology.
All software produced by our lab may be downloaded and used free of charge by academic and other non-profit researchers. Commercial use of the ScanAlyze, Cluster and/or TreeView executable and/or source code requries a license from Stanford University. For information on how to obtain a license, please click here.Commercial use of the GMEP software requires a license from Lawrence Berkeley National Lab.For information on how to obtain a license, please contact LBNL's Technology Transfer Division. Register Here Registration is free, and is used to track usage and to provide software updates. Registration is not required to download software.Microarray Image Analysis ScanAlyze [Download] [Previous versions]:Process fluorescent images of microarrays. Includes semi-automatic definition of grids and complex pixel and spot analyses. Outputs to tab-delimited text files for transfer to any database. Written by Michael Eisen. For Windows only. Manual. Source Code.
Michiel de Hoon of the University of Tokyo has created a version of Cluster (called Cluster 3.0) that implements the same algorithms as my software, but will run on Windows, Mac OS X, Linux and UNIX. It's available here.FuzzyK [Download]FuzzyK is a C++ command line program that will perform fuzzy k-means clustering on gene expression data. See Gasch AP and Eisen MB (2002). Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biology 3(11), 1-22.TreeView [Download] [Previous versions]: Graphically browse results of clustering and other analyses from Cluster. Supports tree-based and image based browsing of hierarchical trees. Multiple output formats for generation of images for publications. For Windows only.
Current version 1.60. Updated December 6, 2002. Maple Tree [Download]Maple Tree is a java-based, open source, cross-platform visualization tool to graphically browse the results of clustering analyses from our Cluster and Fuzzy K clustering software, and many other clustering and analysis programs.Maple Tree was developed by Lisa Simirenko in our lab.
One of the biggest issues regarding this method is the need to remove the noise from the data generated by processing it in the ImageJ software. However, this is not unique to this method as similar noise issues must be resolved with other recording options3,5,6,8. As discussed in the methods, a stationary fly may display minor amounts of movement when processed through ImageJ because the program measures movement from the center of the object, which can vary even in a stationary object due to fluctuations in light and fly posture.
PGEToolbox is a Matlab-based software package for analysis of polymorphism and divergence data for population genetics and evolution. It estimates several basic statistics of DNA sequence variation and carries out statistical tests of selective neutrality under the infinite alleles model, such as Tajima's D test, Fu & Li's tests and Fay & Wu's H test. The significance of tests is determined from the distribution of the statistics obtained by coalescent simulation. The toolbox performs McDonald-Kreitman test (and several extensions). PGEToolbox also contains functions for handling SNP (Single Nucleotide Polymorphism) genotype data. PGEToolbox is open-sourced, can be easily extended or tailored for specific tasks, and scaled up for large data sets.For academic uses, PGEToolbox is available free of charge at
4.1 General Restrictions. Licensee shall not, and shall not authorize or permit any third party to: (a) sell, lease, license, sublicense, or otherwise transfer the Licensed Software or the Documentation; (b) provide, disclose, or make the Licensed Software or Documentation available to any third party, or permit access to or use of the Licensed Software or Documentation by any person other than Licensee's employees, agents, or contractors who are, by agreement, bound by the terms of this Agreement to the same extent as Licensee; (c) merge or combine the Licensed Software with other software, or modify the Licensed Software, or create any derivative software or any other software based upon, or any derivative work of, the Licensed Software or Documentation; or (d) modify or efface any titles, trademark symbols, copyright symbols, notices or legends, or any other proprietary markings on or in the Licensed Software or Documentation. Licensee further agrees that it shall use the Licensed Software solely with data generated using Products. All license restrictions specified in Sections 4.1 and 4.2 and elsewhere in the Agreement shall apply to the maximum extent permissible under applicable law. If Licensee believes that it has additional rights or the right to act contrary to the express license restrictions specified in this Agreement under mandatory laws (including, without limitation, national laws implementing Directive 91/250/EEC and similar laws), Licensee agrees that it shall provide 10x with at least 30 days prior written notice and any reasonably requested information before exercising such rights, to allow 10x to offer alternatives at 10x's sole discretion, for example interface information to achieve interoperability with independently created computer programs.
If required, specimens can be positioned by a 3D-printed micromanipulator [4] (Fig 2B). Up to three manipulators can be attached to the free faces of FlyPi (Fig 1D and 1I). Manipulators can also be configured to hold probes such as electrodes or stimulation devices (Fig 1I). Like the camera objective, manipulators can be optionally fitted with continuous-rotation servo motors to provide electronic control of movement in three axes [4]. These motors can be either controlled via software or via a stand-alone joystick unit based on a separate Arduino-Uno microcontroller and a Sparkfun Joystick shield [19]. Depending on print quality and manipulator configuration, precision is in the order of tens of microns [4].
While not creating a general, flexible software tool, many groups have benefited from automated cell image analysis by developing their own scripts, macros, and plug-ins to accomplish specific image analysis tasks. Custom programs written in commercial software (for example, MetaMorph, ImagePro Plus, MATLAB) or Java have been used to identify, measure, and track cells in images and time lapse movies [10, 22, 23]. Such studies clearly show the power of automated image analysis for biological discovery. However, most of these custom programs are not modular, so combining several steps and changing settings requires interacting directly with the code and is simply not practical for routinely processing hundreds of thousands of images or sending jobs to a cluster. The effort expended by laboratories in creating an analysis solution with a particular software package is often lost after the initial experiment is completed; other laboratories rarely use the methods because they are customized for a particular cell type, assay or even image set. Furthermore, although developing a routine for a new cell type or assay usually requires testing multiple algorithms, it is impractical to implement and test several published methods for a particular project.
Commercial software has also been developed, mainly for the pharmaceutical screening market, by companies including Cellomics, TTP LabTech, Evotec, Molecular Devices, and GE Healthcare [24]. Development of these packages has been guided mainly by mammalian cell types and cellular features of pharmaceutical interest, including protein translocation, micronucleus formation, neurite outgrowth, and cell count [25]. The high cost and the bundling of commercial software with hardware makes it impractical to test several programs for a new project. The proprietary nature of the code prevents researchers from knowing the strategy of a given algorithm and it cannot be modified if desired. As is the case with many laboratories, we have found commercial packages useful for some screens in mammalian cells, but in other cases limiting [1, 5, 26, 27]. 2ff7e9595c
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