There are several types of workstations available in the BioHPC
Laboratory: interactive, remote (general, medium memory, large
memory) and restricted.
Interactive workstations can be used directly in Rhodes 625 the
same way as any desktop computer (with a valid reservation, see
below). They can be also accessed remotely via ssh or Remote
Desktop. Remote workstations and restricted workstations can be only accessed remotely
using ssh (graphical software can be used with remote X Windows or
access documentation). Remote
workstations are more powerful than interactive with most of them having
at least 2 quad core CPUs and are especially well suited for
long and computationally intensive tasks. Restricted
workstations include staff machines, hosted workstations and some regular workstations reserved for special
collaboration or task. Detailed information about hardware
configuration is available here.
Only registered users may access workstations. To request an account
please fill out and submit this Web form, you can also come
BioHPC Lab office hours and set up the account at this time.
Workstations must be reserved in advance, reservations should be
made via reservations web page.
If you are already logged in, you may continue working even after your
reservation has expired,
but your session will be forcefully terminated and all processes killed
when a different user with valid reservation attempts to log in.
Thus, in such a case, it is advisable to re-visit the reservation page and
extend your reservation if time slots are available.
Please remember to remove any reservations you do
not need to avoid blocking access for others and loosing your Lab
Credit Account hours.
Only actually used hours are charged, if you cancel your reservation
before it starts nothing is charged, if you cancel before it ends
only the actual hours between start and cancel are charged. NOTE:
"time used" is defined as the wall clock time elapsed when your
reservation is active - it has nothing to do with how much you
actually used the CPU/RAM etc during this time. "Time used" reflects
the span for which you had the workstation reserved.
You can manage all your reservations from "My
Reservations" web page. This page lists all your active
reservations and provides tools for modifying them or cancelling.
You can also add another Lab user to your reservation, in which case
(s)he will be able to connect to your reserved workstation and work
there, but won't be able to modify the reservation itself. You can
also launch a VNC connection (see "Access") from this page.
You can also end the reservation programmatically by calling
script /programs/bin/labutils/endres.pl with the reservation
number as the parameter. This script must be executed on the
Support and Training
Bioinformatics Facility staff will provide assistance with use of workstations and
software. You can always ask for quick help from CBSU staff (our
offices are Rhodes 616, 618-624), but training and other time
consuming issues should be done during our
Lab office hours. CBSU will run periodic
workshops, and we welcome suggestions
for workshop topics.
Genomic/Sequence Data Transfers
It is possible to use your BioHPC Lab account to receive sequencing
data (or other type of data) from external facilities. Usually we
set up a temporary account for them to transfer data, which is then
moved to appropriate user home directory, please
contact us for more details.
We have a standing agreement with Weill Cornell Genomics Resources
Core Facility, you can ask them to transfer data to BioHPC Lab
storage and they will know how to proceed. Data from Cornell
Genomics Facility can be transferred directly as it is an internal
Aspera SRA toolkit is installed on all computing servers. You can
use it to download SRA data directly into the workstations. Please
SRA guidelines. The toolkit is installed in /opt/aspera,
an example of use is
/opt/aspera/connect/etc/asperaweb_id_dsa.openssh -k 1 -T -l200m