Ver 3.0 of the SDSC image conversion tools have been installed. They allow conversion to and from most image formats on the planet, as well as rotation. shearing, greyscaling, etc. Complementing them are the SGI-supplied to* and from* utilities that also provide much of the same functionality. The SDSC tools mostly start with im and can be listed with ls /usr/local/bin/im*. Each of them has a postscript description (in /usr/local/man/postscript/imtools; view with ghostscript) as well as a man page.
I've just installed the latest version of the mbone tools for multicast audio+video-conferencing. Since mamba doesn't have a video camera, you won't be able to transmit video, but you can receive it, as well as hear the audio portion (though we may have to plug in earphones for it to audible from the chassis. Type sdr & to start it off and wait a few minutes for the sessions to update. Then click on the ones you want to 'attend' and start the appropriate tools from the control panel. While some parts of it may work remotely, it's only really usable from the console. If you want to install it on your own systems, give me a call, or you can try to download and install (SGIs only) it from here .
I've just installed GenomeInspector for your examination. From the announcement:
GenomeInspector is a software package with a graphical user interface designed for comparative analysis of megabase sequences (we tested it with whole yeast chromosomes). However, there is no upper or lower sequence limit. The distribution of sets of genomic structures like open reading frames, transcription factor binding sites, retrotransposons, or any other motifs can be displayed by various means. Any two sets (or more, with a few additional program steps) of structures can also be correlated and sequence elements that are of interest can be extracted. Thus, pairs of correlated elements and their distance can be selected. For the method and short examples, see: Quandt, K., Grote, K., Werner, T.: GenomeInspector: Basic Software Tools for Analysis of Spatial Correlations between Genomic Structures within Megabase Sequences Genomics 33, 301-304 (1996) Due to the versatility of this complex program system, it is absolutely necessary to read the supplied user-guide CAREFULLY, before starting to use the software!!!
Comments from Harry: My initial take on GenomeInspector is that it addresses large scale DNA sequence analysis by allowing compressed views of the sequence, with various analyses overlaid on it, some graphical, some textual. It is graphical, but it is not organized in the "standard" format, so there's some activation energy required to figure out what function does what. The online help works, and will be necessary as the menu selections are not self-explanatory. I'd appreciate feedback from any Genome Gnomes.
Thanks to Brooke Paul, we are now mirroring the PDB files from Brookhaven National Labs every week. They're stored in "/disk11/PDB/All_files" as compressed text files. The Biosym programs know how to deal with compressed files; others may or may not. If a program (rasmol, for example) cannot deal with the compressed format internally, the file will need to be decompressed before feeding it to rasmol. To do this, copy the file to your directory and then decompress it with the gunzip command:
Two new programs for phylogenetic analysis have been addedand are described below. I would be interested in hearing comments from real users...
SEAVIEW (by Manolo Gouy) is an efficient multiple alignment editor. It allows easy gap insertions/deletions into/from selectable groups of sequences. Alignment program clustalw (Des Higgins) can be called on-line, so that (parts of) the sequences may be automatically aligned. A dot-plot routine allows an easy matching of similar regions.
PHYLO_WIN (by Nicolas Galtier) is a graphic interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony and maximum likelihood methods and bootstrap with any of them. Many distances can be used including Jukes & Cantor, Kimura, Tajima & Nei, Galtier & Gouy (1995), LogDet for nucleotidic sequences, Poisson correction for proteic sequences, Ka and Ks for codon sequences. Species and sites to include in the analysis are selected by mouse. Reconstructed trees can be drawn, edited, printed, stored, evaluated according to numerous criteria. Taxonomic species groups and sets of conserved regions can be defined by mouse in both tools and stored into sequence files, thus avoiding multiple data files.
Both are entirely mouse-driven. On-line help makes them easy to use. Most usual sequence file formats are read : CLUSTAL, FASTA, PHYLIP, MASE.
Rasmol Version 2.6 has been installed (as well as rasmol 2.4). Rasmol 2.6 (launch by typing rasmol2.6) is in late beta but seems to be reasonably stable. It has been compiled in 8 bit mode for faster and more compatible graphics (so it can be used - albeit still slowly) to PCs and Macs running X servers as well as to generic X Servers on other unix/Linux X servers. Version 2.6 also has a nice option of 'cartoons' which displays a molscript-like structural diagram of the protein. Version 2.4 is still available as rasmol, but it requires a 24 bit display and therefore is less portable and slower.
Des Higgins' ClustalW v 1.6 is now the default version for clustalw. Docs are in /usr/local/man/text; there is also some primitive online help. type clustalw to start the program. clustalw can write 'msf' files that can be read by SeqVu (Mac) or GeneDoc (PC) for fine tuning and coloration of the alignments. Ask Harry for more info, if wanted...
Harry Mangalam's restriction enzyme program tacg has been installed on mamba in an alpha test. You can get more information by typing tacg -h or by asking for the man page man tacg. The entire manual can be viewed by typing less /usr/local/man/text/tacg.manual. In short, this program provides a great deal of the functionality of the GCG 'map' program but is faster, certainly less costly (free), and runs on Linux. email Harry if you want it for your own or another system.
The latest version of Netscape (V2.0) with Java support has been installed. Use as before.
The GIMP (General Image Manipulation Program) is here! Much like Photoshop, but loads cheaper (free). True GUI image touchup and manipulation. Supports plug-ins. Looks like it will be a widely supported project. Quite usable now (and there's an on-line tutorial, as well. See here for more explanations and links to other GIMP-related info.
The X-based editor Nedit Version 4 is available on mamba (and to anyone else who wants it for their own machine, it can be ftped from here. It is one of the best free X editors for Unix. Type `nedit filename &` to start it. Text documentation can be found, as usual, in /usr/local/man/text. Ver 4 supports rectangular cut+paste, as well as improvements in the previous capabilites (parent matching, drag 'n' drop editing, enhancements via shell programming, some "electric C" options, autobackup, etc).
Version 2 of asWedit, an Xwin, GUI, HTML editor has been installed. It is a free-for-academic-use editor, but pretty impressive in its abilities, especially for HTML, but also for plain text editing. There are versions for just about every Unix platform available for ftp here should you want a version native for your Sun/Linux/HP/etc box
The latest version of BIOSYM/MSI software has been updated. HOWEVER, the old version will continue to be the default until some shakeout has taken place. In order to use the new version, you have to type at the shell (or include in your .cshrc file) the line:
otherwise, you'll get the old (235) version of the BIOSYM pkg. All the standard pkg and all the Life Science Modules have been installed and should be available. If there is strange behavior, please let me know. We need to order new hardcopy documentation to go with it. As soon as I get them, I'll put them in BS 5205. type insightII to start it.
The Spartan Molecular Mechanics/Quantum Code package from WaveFunction has been installed and is available for use immediately. Paper documentation is lacking for the time being although, there is some available online. I'll get paper documentation up to BS 5205 as soon as I receive them. type spartan to start it .
AVS - Advanced Visual System is now available, again without paper documentation. It does have a significant amount of online documentation available. It's much like IRIS Explorer or IBM DATA Explorer ( a visual programming environment), with a lot of predefined modules for analysis, especially image analysis. type avs to start it.
Maple V a symbolic and algebraic analytical tool with extensive graphing tools for external data. Most of its documentation is online. typexmaple to start it
gnuplot - another plotting tool, much simpler and less capable than maple, but somewhat easier to use. Not nearly as easy to use as many of the Mac and PC plotting packages, but certainly more capable than them. Local documentation is available in the standard documentaion places:
./postscript/gnuplot_manual.ps ./postscript/gnuplot_ref_card.ps ./postscript/gnuplot_tutorial.ps
Naomi - Simon Brocklehurst's protein analysis tool, especially useful for visualizing various analyses of protein structure by passing the output thru molscript and raster3d. It's a powerful program and produces both useful data and graphics, but it is driven from the command-line, so you'll have to read about it to see how it operates. Again, documentation is online, via the Web. Look here for the Web documentation.
(I'd advise going thru this page and links to see if it's worth your time to learn it) Local documentation is available in the standard doc places: from /usr/local/man:
A working (if crude) backup system has been implemented, using either an attached or networked 8mm drive. The entire system is backed up every 2 weeks (and tape stored offsite) and nightly incremental backups are done to a different tape. I'll be looking to replace the present software with something more sophisticated.
New versions of ghostscript (aka gs) and ghostview (aka gv) have been installed and tested.
Ethan Merritt's raster3D code has been compiled and installed. The documentation is in man for as well as in html foravs2ps, raster3d, ribbon, balls, render, rods) as well as the Raster3D Home Page, and postscript. It can be used in conjunction with molscript to generate (with some effort) exceptionally good cartoons of molecules. There are also some examples in /usr/local/src/raster3d/examples.
ProsaII (aka prosaII), Manfred Sippl's Protein Structural Analysis tool (for verifying putative protein structures) has been installed. The documentation is in postscript. There are also example sessions in /usr/local/src/ProsaII3.0/data.
namot2, a nucleic acids visualization program from LLNL has been installed. It allows the generation and visualization of 3D models of DNA and RNA in single and double strands, as well as other things. Documentation is mostly by html from the Namot Web Page:
Start the program by typing 'namot2'. It's an X-based program, so don't try it on a Mac or PC unless you're running an X server. Also, because of network latency, it's essentially unusable for dynamic feedback unless you're at the console. If it looks interesting and you have a LinuX setup, it looks like it should compile with minimal changes (but I haven't tried it).
The ImageMagick tools (display, import, animate, montage, convert, mogrify, identify, combine, segment, xtp) have been installed - get info by examining the appropriate man page.
Relatedly, John Bradley's excellent image editor 'xv' is available, as is the postscript documentation.
And also, most of the SDSC image conversion tools are also available (type imconv -fullhelp for the man page).
For Mac users, the new version of MacX (an X server for the Mac) was released today; significant for us because we have a site license which enables UCI users to get it free. Encourage OAC to make it available as fast as possible.
The BIOSYM package can be started by typing 'insightII'. Don't start it as a background job - it needs the starting terminal for input and output. The hardcopy documentation will be available in BSII Rm 5205. DO NOT remove the copies marked with "Mamba". Your internal organs will be sold at auction if you do. Those not so marked can be BORROWED (implies returning) for short periods.
The GCG package can be started by typing 'gcg'. Then type 'genhelp' for the standard character-based help system. If you want to run the X window interface to GCG, type 'wpi'. There is HTML documentation for the GCG package on Unix.
Documentation for the X Windows version of GCG is available HERE:
Joe Felsenstein's PHYLIP has been installed; the plaintext documentation is in:/usr/local/man/text/phylip.
rasmol (Xwin molecular viewer) has been installed (postscript docs online, as the manual and as a reference card and in MS Word format.
Sculpt, an AMAZING molecular modeling tool (requires GL display, installed. If you wish to try the demos, cd to /usr/local/src/sculpt/ and type ./go. Info is available in both as a postscript manual and in plaintext in /usr/local/man/text/sculpt/.
Setor, great GL molecular modeling visualizer has been installed and is waiting for the license to enable it. It has an interface similar to sculpt, and also has a very nice postscript manual
molscript (molecular cartoon generator) installed. Info in plaintext in /usr/local/man/text/molscript.doc.
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