Our Frequently Asked Questions are organized into the following categories:
How do I subscribe to Jellyfish v3.3.1?
You can subscribe to Jellyfish v3.3.1 at any time, during or after your 30-day trial. Your 30-day trial begins as soon as you install or upgrade to Jellyfish v3.3.1. You can subscribe to Jellyfish online at www.jellyfishsoftware.com. To
subscribe, please click "Subscribe" under Jellyfish in the left sidebar
navigation tree. Your subscription payment can be submitted online using our
secure payment interface by VISA, MasterCard, Discover or American Express or
with your PayPal account. We can also accept purchase orders and payment by
check or wire transfer (additional fees apply for wire transfer). If you have
further questions, please contact us.
What should I do if I decide not to subscribe to Jellyfish v3.3.1 after my 30-day free trial period?
You have 30 days to try out Jellyfish v3.3.1. After this trial period, access to and manipulation of your data will only be possible by subscribing to version 3.3.1. If you do not want to subscribe, you should export your files from the program before the trial ends. You can export your data and analyses from Jellyfish as text and JPEG files. If your trial expires before you have a chance to export your data, you can access your data in its XML-format. Please see the File Management discussion below that describes where your data is stored on your computer.
I have just downloaded and installed Jellyfish. When I try to log in, Jellyfish said my trial was expired. How can this be?
Jellyfish trials are monitored by the computer on which Jellyfish
is installed, not by the user login name. Thus, if another user has already participated in a 30-day trial on a computer, then a new user cannot begin a trial on that computer. Please install Jellyfish on another computer to start a new trial.
Is the trial version the same as the subscribed
version of Jellyfish?
yes
I need to work on my
sequences at home and at work, do I need two subscriptions? Do you keep my files
on your server?
You do not need two subscriptions to use Jellyfish
on more than one computer but, because your files are stored on the hard drive
of the computer they were created on (not on our servers), you will have to move
the latest version of your file between work and home. See File Management below to see where your files are stored on your computer. You can use your subscribed username and password to log in to our download page and download another copy of the software to your other computer.
The download stops before it is complete. What is wrong?
This is usually caused because of a
lost connection between our server and your computer. Unfortunately, we cannot
control this. If you are unable to download Jellyfish, please contact us.
Why am I having trouble installing Jellyfish on my Macintosh?
Your Internet browser may not be correctly configured to extract downloaded applications. Jellyfish can be decoded by dropping the downloaded "setup.zip" (MacOS X) file into Stuffit Expander. Most Macintoshes already have Stuffit Expander installed, but if you need a copy please download this free application from www.aladdinsys.com . Decoding the setup.zip file with Stuffit Expander will create an application named "setup" that you can double click to install Jellyfish.
Is Jellyfish available on platforms other than Macintosh and PC?
Jellyfish
v3.3.1 is only certified on PC and Macintosh. For details, please contact us.
Can I use Jellyfish software with a Pentium-MMX processor?
Jellyfish will work on Pentium and Pentium-MMX processors but performance will be significantly slower.
Do I need an Internet connection to run Jellyfish? What if my network uses a Proxy Server to connect to the Internet?
As of release 2.1_8560, Jellyfish can be used in either
"online" or "offline" mode. If you're away from an Internet connection, your
"offline" Jellyfish session will allow you to view your files and use many of
Jellyfish's features. When a network connection is detected, Jellyfish runs in
"online" mode, allowing you to take full advantage of its powerful network
tools, including BLAST searches and GenBank queries.
A proxy server presents no obstacle for Jellyfish. To configure Jellyfish to "see" your network's proxy server, simply start Jellyfish in "offline" mode, and then select "Internet options..." from the "Tools" menu. If you don't know the correct proxy server settings, your network administrator should be able to help you set them. After you successfully configure Jellyfish proxy server settings, your "online" Jellyfish sessions will begin the next time you run the application.
If you cannot start Jellyfish in "offline"
mode, you may not have a current version of Jellyfish. Try downloading a new
version of the application, and try again. Contact us if
network difficulties prevent you from running Jellyfish in online mode.
Where are my files stored? How can I access them?
You can directly access your
files without going through the software, as they are all stored on your hard
drive. Field Scientific does not have a copy of your data and analysis - it is only stored
on your computer. We suggest that you back up your data and analysis
periodically. Typically, your files are stored in a Users folder in one of the
following locations:
Users who initially downloaded Jellyfish after v2.1:
Users who initially downloaded Jellyfish v2.1 or an earlier version:
Does Jellyfish v3.3.1 allow file sharing?
No. Your data and analyses are stored on your computer and access to these files is granted based upon your login ID and the computer. For example, if different users access Jellyfish with different login IDs, they will each see their own filing system. Also, if you access Jellyfish from another computer with your login ID, you will see the file system you have stored on that computer. To share data and analyses with colleagues, export these files as text or JPEG files.
I have just upgraded to a new computer and have installed Jellyfish on it. How do I copy my files?
The most effective way to transfer your files is to drag the entire Users folder onto a disk or flash drive, and then drop that into the appropriate location on your new computer. It's necessary to copy the entire Users folder because there are certain files within this folder that Jellyfish needs in order to recognize your projects. Please see the first topic under File Management to locate your Users folder.
How does Jellyfish calculate the melting temperature of oligonucleotides?
Jellyfish uses three different methods to calculate
oligonucleotide melting temperatures. The first method, which is a good
approximation for oligonucleotides that are 20 bases or less, is the Wallace
calculation (1):
Tm = 2oC(A+T) + 4oC(G+C) = Tm (basic)
> The second method that Jellyfish uses to calculate melting temperatures is the GC Content method, also called the long probe method (2). This approximation takes into account the length of the oligonucleotide and salt concentration and is suggested for Tm estimations of oligonucleotides longer than 40 bases.
> Tm = 81.5 + 0.41(%GC) + 16.6log[M] - 600/L = Tm (GC content)
The third melting temperature calculation is the thermodynamic-based nearest neighbor method described in Rychlik et al. (3) and Breslauer et al(4). This most accurate method accounts for the effects of base stacking, salt concentration, and oligonucleotide concentration and is expressed with the following equation:
Tm = (dH / (dS + Rln[c/4])) - 273.15 + 16.6log[M] = Tm (nearest neighbor)
where dH is the sum of the nearest neighbor enthalpy changes, dS is the sum of the nearest neighbor entropy changes, and R is the gas constant (1.987 cal deg-1 mol-1). The default concentrations for all Jellyfish melting temperature calculations are 50 mM salt concentration (M) and 50 nM oligonucleotide concentration (c).
>
(1) Wallace RB, Shaffer J, Murphy RF, Bonner J, Hirose T, and Itakura K (1979) Nucl. Acids Res. 6: 3543-3547.
(2) Howley PM, Israel MF, Law M-F, and Martin MA (1979) J. Biol. Chem. 254: 4876-4883.
(3) Rychlik W, Spencer WJ, and Rhoads RE (1990) Nucl. Acids Res. 18(21): 6409-6412.
(4) Breslauer KJ, Frank R, Blocker H, and Marky LA (1986) Proc.Natl. Acad. Sci. USA 83: 3746-3750.
Where does your restriction enzyme database come from and how can I add new enzymes?
Our
restriction enzyme database was originally mapped from NEB. Unfortunately, you
cannot import from Rebase. If you'd like to see additional sites added, feel
free to contact us.
How do I perform other analysis such as promoter searching?
In terms of searching for promoter regions and transcription factors, you can use the relevant WebTools to perform such analysis. To obtain confident results, we recommend that you submit your sequence to several different sites for analysis and compare the results.
Can I suggest new features and functions for future versions of Jellyfish?
Please do!
The direction that we take for further development is influenced by your
feedback. We would love to hear your comments and would appreciate the
opportunity to work with you to develop new tools and features. Please send your suggestions to us.
