Before downloading
YUP
You need to
have a supported platform. See the list in the next section.
You need to have version 2.4 of the Python interpreter installed
(versions 2.3 and 2.5 will not work).
You also need to be able to view Portable Document Format (PDF)
files as the installation instructions are in this format. Python and
PDF software
are part of standard installations of the supported platforms. If
you are reluctant to install Python 2.4 but you have UCSF Chimera
installed, you can "borrow" the python interpreter that is installed as
part of that package (chimera/bin/python2.4).
The graphical user interface and molecular viewer are not delivered
with this distribution of YUP. For now, we are using the KiNG Kinemage
viewer to view molecular structures. You can obtain and install KiNG
from the Richardson
Laboratory at Duke University. |
Availability
At this
time, YUP compiles and work correctly only under UNIX-based operating
systems. (We hope to fix this in the future, but it is not a priority.)
YUP is
available on four platforms for now:
| Hardware |
Operating System |
Python Versions |
| PowerPC
(G4 and G5) |
MacOS
X 10.4 (10.5)
|
2.4 |
| Intel
Core 2 Duo x86 |
| 32-bit
x86
(Xeon) |
LINUX (RHEL3) |
| 64-bit
x86
(Core 2 Duo) |
LINUX (Ubuntu 6.10)
|
Only
the hardware and software variants that we have tested are listed.
Other variants (other LINUX distributions, AMD processors, MacOS X
10.3) may work as well. Available for MacOS X 10.5 are Universal
binaries
and these are slightly faster than the regular versions but they have
not been widely
tested. The Installation Manual provides instructions on how to avoid
this version. Support for Python 2.5 should be completed by the
end of 2008; try installing
Python 2.4 (it is easy if you use the MacPorts or Fink distributions)
to be used with YUP. Note
that only the Python
sources are
included; there is no "C" source, so this package can never work on
unsupported platforms.
|
Release
Notes
These can
be found here. |
Uses of
YUP
This
package contains three model types: [1] reduced representation or
simplified RNA and [2] reduced representation DNA, [3] Emmental, a
model for fitting into density maps and [4] VirPack, the
virus packing model, mentioned in the JCTC paper, will be made
available in a later version, really. (The other model
types included with the package are programming samples.) If you are
going to use either reduced representation model
types, then you can install YUP and use the package right away. You
will need some knowledge of the Python scripting language.
YUP is designed to make it easy to implement new model types. This will
be a trivial task if you are fluent in Python and familiar with
object-oriented programming. |
Obtaining
the YUP Package
There are
three ways to obtain the YUP package.
| 1: UNENCUMBERED version 1.080626, dated
June 27, 2008, DOWNLOAD |
This
is the latest release,
and is available without prior registration. However, we do encourage
you to tell us who you are: register.
You will
download
a file
named YUPxxxxxx.tgz where xxxxxx are six digits. Make sure
you do not have a file with the same name in your download directory. |
| 2: ENCRYPTED version 1.080101, dated
January 2, 2008, DOWNLOAD |
(You may have to
right-click on the
download link and you have to remove any name extension that your
browser might add to the file.) This
is a placeholder for an older
release,
and you need to obtain a key to decrypt it. Your download is a file
named XXX-YUPxxxxxx-tgz-XXX (watch out for browser
modifications to the name) where xxxxxx are six digits. Make sure
you do not have a file with the same name in your download directory. If the following procedure
does not work, use the registration form for the unencumbered version
to reach us. Otherwise, to obtain the
password by the quickest method,
send
an email to:  , put
"Request for Key" in the
subject line and some information about yourself:
|
| New Registrations |
Registered Users |
| Please give your [1] full
name, [2] affiliation (company or institution),
[3] postal address, [4] number of installations per platform, [5] email
address. We need just enough details so that we can determine that your
request is genuine and we can identify you in future requests. |
If you have received a
password from an earlier request, you need a new one for this
download. You only have to give as much information as is necessary
to identify youself. For example, if you have a commonly used name,
identify
your affiliation as well. |
| The text of the command to
decrypt the download will be mailed to you (therefore, make sure your
email address is valid). Copy the command and paste it into a terminal
window, in the directory that contains the downloaded file, and run it. |
3: Members of the HARVEY LAB
|
SFTP to SNARE, cd to /LNX/600/curator/ and get the highest numbered version of
the YUP package, which is not encrypted, and which may be more recent
than the official release. |
The
downloaded file contains Python source code and compiled binaries
of shared objects for all the
supported platforms.
The C source code for the shared
objects are available only by request and only as a disk
image file for MacOS X. (The C sources are not for the faint of heart
anyway.) |
Extraction
and Installation
Your
browser will most likely extract the unencumbered archive for you. If
you have to
extract the package yourself, type the command:
tar -xzf YUP.tgz
where YUP
Inside the directory, you will find a PDF file Install-YUP.pdf. Follow the instructions in
this file to install YUP. |
Learning
to use YUP
Work
through the tutorials to learn
to use YUP. A separate tutorial exists for Yup.scx. |
|