Research Support
FAQ
General Questions:
1. I have a file that is larger than the 10 MB limit for e-mail attachments. How do I transfer this large file to a colleague at UMDNJ or another institution?
Ans. Use the UMDNJ Large File Transfer Service (LiFT). To view documentation click here. To access the Large File Transfer webpage click here. To login UMDNJ faculty must use their email address and portal password.
2. How do I get an account on the Scientific Server? Ans. See the Sci Server home page for more information.
How do I reset my scientific server password? Ans. Go to https://ironclad.umdnj.edu/scientific/resetpw to reset your password using your e-mail account credentials.
3. I am a new user of the high performance SAN. How do I transfer files and work in unix? Ans. Get a copy of the UNIX workshop.
4. How do I move my project directory along with everything in it (including subdirectories) from my linux workstation to the scientific server? Ans. This topic also falls under the category of archiving. In unix systems, you have two very powerful commands for archiving and compressing whole directories of data. We want to archive and compress so we transmit a minimal size file across the network. Here is how to do it on most unix systems:
tar cvf - mydir | gzip > mydir_files.tgz (where mydir is the name of your project directory!)
Now use securecopy to copy the tgz file (affectionately known as the "tarball") to the scientific server (siriusc) ...
scp mydir_files.tgz username@siriusc.umdnj.edu:/users/username
Login to siriusc and extract the tarball ...
gunzip mydir_files.tgz (gives mydir.tar)
tar xvf mydir_files.tar
See the UNIX workshop for more information.
5. I have an account on the scientific server and on the V12 linux lab in Piscataway. How do I access the Piscataway V12 lab linux workstations either from Newark or remotely?
Ans. In Newark, use the VNC client (Go to Informatics Institute VNC client page for more information). Remotely, you must tunnel your VNC session through SSH. Alternatively, you may tunnel Reflection X through SSH (See the How To - pdf).
6. What does "disaster recovery" mean? Ans. In our environment, disaster recovery means that data is backed up to tape nightly and stored for a period of 7 days. The back-up tapes are recycled and used again. So, if the system disks crash and cannot be recovered, your recent data store can be recovered.
7. What if there is a storage system failure during the day while I am working? Will my data be lost? Ans. Your work or data generated for that day will be lost unless you make your own back-ups during the course of your work.
8. What if I remove or delete a file on the unix system? Will I lose this data? Ans. Unless the data was generated the day before (therefore it will be on our back-up tape), new data generated the same day and deleted by the user the same day will be lost. Always exercise caution when removing files on unix systems.
Molecular Modeling:
1. Are there graduate level courses available in molecular modeling at UMDNJ? Ans. Yes! See the course offerings in the Informatics Institute coursewebpage.
2. What is homology/comparative modeling and how can this technique benefit my research project? Ans. Homology or comparative modeling as it is more commonly referred is a technique whereby one uses a known template x-ray crystal structure of a protein (from the PDB) to build a 3-D structure of a related protein sequence. The protein sequence in question must be in the same family of proteins as the template and must have a sequence identity of at least 25% with the template sequence. The 3-D structure obtained can be used to study the structural impact of mutations or enzyme mechanisms, etc. using molecular dynamics techniques. Contact John Kerrigan, Ph.D. at 5-4473 or via e-mail for more information.
Sequence Analysis:
1. Are there graduate level courses available in sequence analysis? Ans. Yes! See the course offerings in the Informatics Institute coursewebpage
2. Where can I find tutorials for EMBOSS? Ans. See the Informatics Institute resource for EMBOSS here.
Statistics:
1. How do I obtain SPSS or SAS for Windows? Ans. Contact Gary Masson at 2-5942 or via e-mail at massonga@umdnj.edu
2. What is R? Ans.R is an open source statistics package. You may download R from http://www.r-project.org/ Caution: R is for more advanced computer users.
