Question: I have a new post-doc, molecular biologist in the lab who will need to perform GeneBank searches and sequence analysis in the near future. I have not had a need for this capability until now and therefore have never had a "VMS" account. Although I am generally pretty naive about this stuff, it appears to me that full search and analysis cababilities are now available to the general public on the Internet via centers like NCBI. If this is correct, is there still an advantage to having an Alpha account to do sequence searching and analysis?
Answer: It is true that if you know what you're doing and have the time to keep track of changes around the Internet, you can do via the Internet many of the things you can do on the RCR computers. The catch is that you or someone needs to keep current on what is out there and how to use it (most sites have their own peculiarities and not all are intuitive, even to those of us who spend lots of time out there).
Using the RCR provides you with a higher level of consistency, both because of our efforts and the fact that most of the work can be done within the GCG suite of sequence analysis programs. The consistency is certainly not perfect, but it's better over all that cobbling together pieces from a variety of web sites around the world.
Also, although database searches of various types are readily done, other kinds of analyses are less easy to do -- if even possible. You also generally have less control over formats and output and less access to multiple options, for example, searching only a portion of a database or a database comprised of sequences that you've put together because they are important to you.
Of course, there are some things we can't do that can be done via a web site. In these cases, we try to have an idea of where such things are and how to use them so that you don't have to waste too much time trying to figure out everything. Furthermore, if we don't know, we try to find out ways to accomplish a given task.
This point brings up what we think to be the most important reason for having an account with the RCR: you have access to the knowledge and resources of the RCR staff. Most people doing molecular biology here have found that the information they get from John Hill's course, the postings and other handouts, and group or individual consulting sessions saves them enough time to more than justify the $475 per year that it would cost a lab (the whole lab -- with each person getting their own account).
The RCR also maintains a copy of GeneWorks on the Mac in MSB-174 that is available to RCR users. Most people don't use it very much, but for certain tasks it can be the best choice.