The primary management objective of the Computational Biology Core Facility is to maximally advance research and education related to core expertise for our affiliated members. The organization of the facility is predicated on the assumption that computational techniques will be increasingly important for state-of-the-art biological research. We also recognize that students, faculty, and staff within the institutions that the core serves have a wide range of existing expertise, needs and resources. For this reason, the core use policy is designed to be as organizationally flexible and adaptive as possible.
It is important to minimize barriers to use of core facilities, especially for new projects and laboratory groups just learning to incorporate computational techniques into their research. For this reason, the Directors of the facility will continue to seek funding to provide, as far as possible, open and free access. At the same time, we recognize both the need and the value inherent in receiving direct support from research groups making heavy or central use of the core facility.
The transition from free use to pay-as-you-go use is probably best understood in the context of the three tiered level of support around which the facility is organized and managed:
- Tier 1: Tier one support refers to use basic use of software and hardware with minimal expenditure of staff resources. Software and hardware are made freely available to anyone with a need. The facility maintains a large array of software of general interest to the community. Some of this software is free, while some requires yearly site licenses. With fee for use software, we evaluate the likely general usefulness of the software and invest accordingly. We are particularly mindful of opportunities to maximize the value of the investment across institutions. Core purchases have already saved individual laboratories multiple thousands of dollars. Occasionally users request additional software to support specific lab groups. Freely available software is obtained and installed at no charge. If there is a charge for the software, we pay in full, partially pay, or request payment from the requesting lab based on our assessment of the likely general use of the software as well as the ability of the requesting laboratory to pay.
- Tier 2: Tier 2 involves training beyond basic installation and creation of user accounts. Core facility staff organizes educational workshops focused on specific software packages and/or computational techniques. Workshop topics are established based on the perceived needs of the community by the staff and occasionally on requests from users. In many cases experts are brought in from outside San Antonio to lead these workshops. To date, all workshops have been free and the expectation is that most or all will continue to be free.
- Tier 3: Tier 3 involves direct investment of staff or affiliated faculty expertise to support research. At this level of support, a staff member participates directly in computational efforts in individual laboratories as full collaborators. The initial establishment of Tier 3 efforts is not explicitly dependent on the prior existence of funds to pay for the service. However, as these collaborations frequently result in the generation of new grant proposals, we then work with PIs to include support for the facility in those grants. An important measure of the success of the facility is how well it incubates new research directions and contributes to successful new grant applications. PIs whose projects are heavily dependent on the core's services are expected to include support for facility staff, software and hardware in their grants. Well funded PIs who make heavy use of core services are also expected to support the facility. The ability to provide intensive Tier 3 support at little or no cost depends on core funding.
Although at present the facility is not used by businesses or outside organizations, we anticipate the possibility of such use at any of the three levels identified. Decisions about fees for services for outside groups will be assessed on a case by case basis. At no time, however, will the ability of an outside organization to pay for services exclude use by affiliated organizations (at present UTSA and the UTHSCSA). The principle focus and the top priority for use will always be given to members of affiliated organizations.
In summary, the Computational Systems Biology Core Facility is not designed or intended to be a profit center. The facility is constructed as a collaborative, intellectual / scientific enterprise that focuses on supporting research and incubating new research directions. While we expect and encourage our users, especially those with the means to do so to contribute to core operation, we also anticipate that core services will always be subsidized by sources of support obtained by the directors themselves, as well as by the institutions served.
As part of our mission to provide computational infrastructure to researchers, data storage is provided only as needed to conduct research and data analysis with our hardware. At no time can any data that is classified as Category I/Confidential be stored on our systems. Any data of a personal nature(musics, videos, pictures, etc) nor any backups of software or backups of lab equipment may be stored. Under no circumstance may illegal and/or pirated material be stored.
Primary Investigators(referred to as Data Owner in UTSA's policy) are responsible for their research data and its management. As part of our infrastructure we have disaster recovery methods to ensure proper and smooth operations, yet these are not available to the user. As such we cannot be considered a backup, thus it is the responsibility of the Data Owner to maintain a proper backup of their data.
All users of our services have access to a personal directory or home directory accessible to only themselves. Under certain circumstances, the PI may request to have access to a subordinate user's directory as part of their data management. Administrators may also access the home directory, but only as part of their duties to maintain system integrity. All users are considered 'Standard Users' and as such are capped at 100GB per home directory. Under special conditions may a user be considered "Advanced" and allowed a higher cap, as determined by the Core Director.
Once a user is no longer affiliated with the University or after six months of inactivity, or we are notified by a PI, a user's account will be marked as inactive and locked. Data held within the user's directory can be made available to the PI for their data archive procedures. After another six month period, any remaining data will be declared abandoned and removed from the system. If the user returns to the University, their account may be reopened, but once data is declared abandoned, there is no guarantee of recovery.
Group shares are available as a means to share data between members of a research group or lab for collaborative work. The same restrictions as to what can be stored apply here as well. At no time can this location or the home directory be considered a place for long term storage. Once a procedure is implemented, storage will not only be capped by capacity but by age as well.
Soon to be available will be our long term archive system. Only PIs/Data Owners will have access to this system. PIs will be able to apply for storage on a yearly renewable basis and a recovery fee may be applied. Again the same restrictions on what is allowed is applied here as well.
Typical Use Cases
- Home: User would store data/work/and results here. Maintain a directory layout that keeps files organized. Having hundreds of files within a single folder(not counting sub-folders) can slow file navigation. Older data/files moved to external storage and/or given to PI for archival.
- Group: Maintain central copy of data set for lab/group research. Users share files with other lab/group members in this location. Older data/files moved to external storage by PI for archival.
- Archive: PI access only, for hosting old and/or large data sets for long periods of time.
The CSBC maintains two rooms, the classroom and the workroom, for users who need access to high end workstations for their work. We require all users to sign in at the front door via the touch screen, which is good for a single day.
Food and drink are allowed in small quantities and we ask that all users clean up after themselves. Please report any spills, though should users disregard this, then we will ban all food and drink. Please use the trash cans in each room, and there is a paper recycling bin by the printer.
Cell phones are not prohibited but we ask that users please take their phone calls outside of the lab. There is to be no propping open the front door as this is both a security and fire safety issue. Only approved users are allowed in the lab after hours.
All the workstations in the workroom are Windows XP and require a user reserve time beforehand. Any user found using a system without a reservation will be asked to reserve the rest of their time. Should a user be using a system that is reserved by another user, they will be asked to move to another system.
All the workstations in the classroom are Linux and do not require a reservation. While users can lock the workstation, we ask that we be notified. Users are allowed to bring their laptops, but note that there is a limited number of power and network connections. Under no circumstance should a user unplug a power or network cable. Air Rowdy is available to all UTSA students, faculty, and staff.
The IPA license renewal is near and the terms under which users can access IPA will be changed. An updated policy will be posted once available.
When using MATLAB, it checks out a license from the pool of available licenses as well as a license for any toolboxes in use. As there is a limited number of MATLAB licenses, and in some cases even less for some individual toolboxes, there is a usage policy in place to promote fair usage for all users.
When using MATLAB, please restrict your usage to only a few instances as needed. The more instances in use, the less there are available for the rest of the community to use. We encourage you use MATLAB in this fashion when actively developing code. Once your code is ready to run full computations, there are two options to run your code that does not use a MATLAB license.
MATLAB code can be compiled into a stand alone executable that does not use a license when in use. It can be submitted to the cluster as a normal serial job.
Also available is the MATLAB Distributed Compute Server(MDCS) that can accept MATLAB jobs in much the same fashion as a traditional cluster. This is advantageous for running many individual jobs or running large parallel jobs. Running MATLAB code this way only uses a single MATLAB license when interacting with the MDCS.
MATLAB license usage is monitored and those who do not follow the policy will be notified.
All users must reserve a workstation ahead of time and be aware that storing data within the Windows profile (i.e. Desktop, My Documents, etc.) is strongly NOT recommended as that data is not protected and also leads to long login/logoff times.