It's been a while since we've communicated with our subscribers
and we've got a lot to tell you about. There are a number
of new services we are rolling
out in the Fall, new staff joining the SACS
team, and several updates to the software and databases you are
already using. We've also been having discussions about how best to serve
our community of users, what services to offer, and what the ongoing
research and support needs are, but we decided that a good first step
was to ask our users! We've set up a
survey that we'd
like you to fill out. It's the multiple-choice
variety, so it should be quick-and-easy and would really help us
adapt and enhance our services, so please take the time to let us
know what changes you want to see.
Survey URL: http://www.sacs.ucsf.edu/cgi-bin/surveyCGI.py?../datadocs/sacs05.xml
By the way, one of the questions we have on the survey is whether we should consider renaming SACS. The Sequence Analysis and Consulting Service was a great name when we set SACS up, but we, like the field have moved well beyond sequence analysis and are involved in a number of projects from genomics to data management to web visualization. If you have any ideas for a great name, or if you just don't like change and SACS is fine, let us know!
We should mention, that while we're updating and adding many services, it's worth noting that many things aren't changing: we still offer up-to-date bioinformatics databases and software, we still provide e-mail suitable for research uses (no attachment limitations, multi-platform support), we still provide access to relevant USENET news groups, and we still provide access to an environment that can be used to develop your own bioinformatics software or scripts.
We hope you find this newletter useful! We have designed it so that readers can link directly to the information that they are interested in or browse the entire newletter to see what's going on. If you have any suggestions on topics you are interested in, or ways that we can improve our communication with our users, let us know! We hope to publish this Newsletter every other month, so suggestions for content would be appreciated!
| John "Scooter" Morris, Ph.D. | Susan Jean Johns |
| scooter@cgl.ucsf.edu | johns@cgl.ucsf.edu |
Welcome to John "Scooter" Morris, Ph.D., who joined the RBVI (Resource for Biocomputing, Visualization, and Informatics) as Executive Director. As you know, SACS is part of the RBVI along with the Computer Graphics Laboratory. Scooter joined us last year after spending the previous 19 years at Genentech architecting, building, and managing their infrastructure and participating in numerous projects. Scooter has undergraduate degrees in Computer Science, Physics, and Biological Sciences from the University of California, Irvine, and received his Ph.D. in Medical Information Sciences from UCSF working in the Computer Graphics Lab. As you can see, this is sort of a homecoming for him!
As Executive Director, Scooter will be working with Tom Ferrin, the RBVI PI, and others to help with the administrative and managerial aspects of the resource, including SACS, as well as lending a hand in the ongoing research and operation of the lab. Scooter is interested in Human-Computer Interaction (HCI) and problems involving biological data management and visualization, particularly web-based visualization. He has joined Susan in the SACS Mission Bay offices in Genentech Hall (GH N476A).
One of our goals is to continue to deliver value to our subscribers. As technology has moved forward, we have realized that we need to review and enhance our offerings. The goal of SACS is to support biomedical research, and while we are not an ISP or a general IT provider, we recognize that SACS plays a role in providing infrastructure services in support of research along with specialized tools and expertise. Security is always an important topic, and we have enhanced our security through Virtual Private Network capabilities as well as through ability to utilize a Single Sign-On environment. Together these provide additional security and additional convenience.
The degree and number of collaborations is also increasing, and the need to share data between collaborators increases along with it. Sometimes you can just send a mail message to a collaborator with the data included, but often you want to communicate with a group of collaborators. Sometimes, e-mail is still the right option, but maintaining distribution lists and tracking comings and goings can be difficult. One solution is to set up an e-mail distribution list that collaborators or other interested parties can subscribe to. Another option is to set up a separate web site for your collaboration or lab that includes direct access to the data. Now you can also include applications on your web site which can control data access, or provide collaborators your results or analyses as they become available. Finally, sometimes, the easiest thing is just to make the file available on the network. You can set up a large network-accessible disk for your lab which can provide shared access to documents, data, or applications.
At the end of the day, we all need to disseminate our findings, and one of the common ways of communicating our results is via posters. The RBVI has now purchased a high-end poster printer that is available to SACS subscribers. No more trips to Kinkos!
We hope you find these new offerings useful!
Virtual private network (VPN)
A Virtual Private Network (VPN) is a way to set up a secure channel between a computer and another computer or a distant network. The idea is to use the public internet to send private traffic by encrypting the traffic. We have implemented a VPN using a hardware device sold by Cisco Systems that allows us to have have a VPN between computers on the public internet and the UCSF network.
One of the great benefits of a VPN is that your computer appears to programs at UCSF as if it were actually on UCSF's campus network. This provides full access to the UCSF on-line journal subscriptions, as well as any services which are limited to on-campus users such as our SAMBA services discussed below, private web sites, etc. Of course, the major benefit is that *all* of your traffic between your home or laptop computer and the UCSF network is encrypted. This provides a very high level of security that is difficult to acheive without technology such as a VPN.
This service is provided to SACS subscribers as part of their base subscription, and no additional software or hardware purchases are required to take advantage of this service.
You must install the VPN client software on your home or laptop computer, and you must change (or have recently changed) your password using the new change password web page (see Single password for details). The client software is available for Windows, Macintosh, and Linux computers. To get detailed instructions and the necessary software for setting up your home or laptop computer for the RBVI VPN, see the RBVI VPN "How To" Guide.
Privately managed e-mail distribution lists
We've all used distribution lists -- either we've set them up in our own e-mail client, or we've subscribed to them over the Internet. We will make available a web-based tool called mailman that can be used to set up public or private distribution lists, including the ability to moderate and archive the traffic.
Mailman can be used to set up lists of lab members, collaborators, or simply interest groups in a given scientific topic. Public lists can be subscribed to by external parties without you or members of your lab having to do any administration. Postings can be moderated (i.e. have to be approved by the list owner) or unmoderated.
This service is provided to SACS subscribers as part of their base subscription, but you will have to provide the person to administer the list.
There are a couple of steps required to set up a new list. First, SACS staff will need to be informed of the list so that they can enable it and modify the mail configuration accordingly. As part of this setup, you (or a list administrator you designate) will be provided access to the administration page for the list, where all of the parameters for the list operation can be set up. Then you can advertise your list! One word of caution, however: we have found that the most time consuming part of list administration is going through and deleting the spam that comes to the list. Generally, this spam is not sent out to the list participants, but it does take 5 or 10 minutes once a week to tell the list to discard the accumulated junk.
Network-accessible disks (SAMBA)
A network-accessible disk is simply a section of disk space on socrates that can be mounted like a network disk or share on your PC or Mac (or Linux) desktop. We have purchased a large amount of disk space to support this service, and each SACS group will have access to 50 GBytes of disk space. The space will be available on socrates just like your current space, but it will have a slightly different path (/home/socr/c/nobackup) to facilitate "exporting" it. We use software called SAMBA to make the disk space available to the network and your desktop. By default, the disk is only accessible to members of your group, and even then only from the UCSF network (although you can access it from home using the VPN).
A couple of caveats, though. While these disks are very reliable and have built-in redundancy (RAID), we can not afford the additional labor to back them up on a regular basis, so you should keep a copy of any really critical data on an additional disk or on some other medium. Second, at this point, we don't have an easy way to delegate the administration of who has access to these disks. While we're happy to make changes to the security configuration of the SAMBA export, we are resource-limited, so we want to minimize the number and frequency of such changes.
Network disks provide a convenient way to share data or just have a central repository of important documents. You can use it to back up critical data (keep a copy -- see the caveat above), or just to extend your disk space. You can also use SAMBA combined with the VPN to transfer data from work to home and back. We suspect that this is one new service that our users will have no problems finding uses for!
The 50 GBytes of space is included in your SACS subscription. Any requests for special backups will have to be paid for by your lab to cover our labor costs, and any additional space will be charged at $.25/Mbyte, which is 1/2 the normal rate for disk usage in your "home" directory.
This will be activated for each group automatically in September. In order to take advantage of it, you will need to have recently changed your password (see the section on single password), and then you will be able to mount the disk as "\\socrates.cgl.ucsf.edu\sacs-nobackup" on the PC using "Map Network Drive..." under "My Computer" and on the Macintosh by using "smb://socrates.cgl.ucsf.edu/sacs-nobackup" from the Finder. You will be prompted for your username and password, and then the disk will mount. You will see a list of folders for all SACS labs. Find your lab (labs are organized by the UNIX id of the lab head), and click to go into it. After that, you are set to go!
Single password for all services
We all have lots of passwords to remember, and we keep getting asked to provide them. We have done two things that should lessen the hassle associated with passwords. First, we've set things up so that when you change your password using the password change page, all passwords associated with SACS services will change. That way, at least as far as SACS is concerned, you will only have one password to deal with. Second, for those who wish to take advantage of it, we've implemented a "single sign-on" system that allows you to log into your PC or Mac using the same password as you use for SACS services, and in doing so can get onto socrates or SACS web sites without providing your password again.
The "single password" feature simply makes things easier, and it is now the default way that our system works. Single sign-on represents a slightly more involved procedure to activate, so you would only want to use single sign-on if you used SACS and/or socrates for lots of computing activity. It is a significant convenience, but certainly not a necessary feature for all users.
Both single sign-on and the single password capability are part of the standard SACS subscription.
In either case, you need to go to the password change page and change your password. This will activate your network-shared disk account and allow you to use the VPN. If you do not wish to take advantage of the single sign-on, that is all you need to do.
To take advantage of single sign-on, you will need to make some changes to your system configuration. The "How To" instructions provide a step-by-step procedure for enabling single sign-on for your platform. Note that for some platforms/features, this will require administrative access to your system and may require one of the RBVI administrators to do some configuration.
Poster printer access
An Epson STYLUS PRO 9600 large format printer capable of printing poster-sized images up to 44 inches wide at very high resolution (2880dpi x 1440dpi max) available to SACS subscribers.
This is an easy one; this poster printer provides equivalent (if not better) quality as Kinko's or any other commercial poster printer at a substantially reduced cost. Better than that, it's here at Mission Bay and you can take a look at it right away. The inks and paper are high quality, but we do not have that capability to laminate the posters, so if you want something laminated, you will still need to send it out to a commercial shop.
One standard-sized poster (3 foot by 4 foot) per month is included as part of the SACS subscription. Because the supplies are so expensive, we do need to charge for additional posters. Based on our estimated supplies costs, additional posters will be charged at a rate of $5/linear foot, so an additional 3' X 4' poster would cost $20.
First, read the Poster Printer "How To" Guide for information about setting up your application to use this printer. In general, we recommend that you use the PowerPoint templates provided to avoid any unfortunate surprises with resolution or page size. Once you have your document, with the page setup set to the appropriate size, mail your document to posterprint@cgl.ucsf.edu and one of the SACS staff will queue your job to the printer, then come on by to pick it up (Genentech Hall, room N453).
Changes to disk space policies
Ever been worried about disk storage charges? Now you can relax. Starting 9/1/05 there will be more free space to work in. A group's backed up disk storage will be increased to 100 MBytes. Think of this as your data archive. Additonally, associated with each group account there will be a 50 GBytes SAMBA mountable scratch space. 50 GBytes in which to test out theories, explore ideas and interpret results. Data of interest would then be stashed away in your archive. SAMBA details available in the Network-accessible disk article.
Have a computer savvy member of your lab that just keeps pounding out really neat analysis tools? Want to share these tools with collaborators via the web? Now you can. SACS has long hosted group web sites. But, in order to put up your own analysis tools you had to go through hoops and have SACS staff install your tool on a SACS page. No more. Let your little genius loose in your own group web site starting 9/1/05 to put up existing tools or create new ones. Show off their work to the world. Interested? Contact SACS to convert your old SACS web site or launch a new one.
Keeping competitive is the name of the game. In this fast paced world, things keep changing. No where is this more true than in bioinformatics. Recently, FASTA has been updated to version 3.4t25 (5/05), EMBOSS is up to 3.0.0 (7/05), and Phylip has just released 3.64 (7/05). All these updated releases have been folded into the SACS resource. So whether you are a command line user or utilize SACS web pages, these updates are at your finger tips.
The long awaited new release of GCG is due out this summer. Now called Accelrys GCG, release 11 promises new and updated aligorithms, the ability to use larger sequences and SeqMerge, a new fragment assembly tool.
Additionally, R and CE have been added to the resource (command line only). R provides an integrated suite of software facilities for data manipulation, calculations and graphical display. It includes operators for calculations on arrays, a large number of tools for data analysis and is highly extensible. While some consider R a statistics system, its authors feel that it is an environment within which statistical techniques are implemented. CE is a means for calculating pairwise structure alignments using the combinatorial extension method. CE requires no previous knowledge of equivalent positions and can be a valuable tool in establishing evolutionary relationships between proteins that share little or no common primary structure.
Traditionally, SACS has held their seminars/classes in the Library's S165A facility on the Parnassus campus. Starting this fall that changes. A new training facility is being established within the RVBI at Mission Bay. A cozy classroom with a high end projector and desktop computers located in N453 Genentech Hall will be the new home for SACS seminars. So if a seminar topic interests you, do stop by.
Have questions that you want answered NOW? Contact us. SACS is reachable by phone (476-5379), by email (sacs@cgl.ucsf.edu) and of course you can stop by the office at N476A Genentech Hall during regular office hours. The SACS web site have numerous "contact" links where you can email us your comments or questions.