BCBC – Infrastructure
William and Boyce
The bioinformatics team has installed a new server, called “William.” It runs Ubuntu Server Linux and has 128 GB of RAM, 64 cores, and 6 TB of disk. It is suited to run smaller jobs, such as BLAST and NGS read mapping, that do not require the power of “Boyce,” the large memory machine. The Boyce server is designed to run larger jobs. If staff plan to run smaller jobs, they may want to request an account on this new William system to free up Boyce for the larger tasks.
All BTI staff are welcome to use the new server at no cost. Staff are encouraged to schedule their use of the server using Google Calendar. Researchers can plan and reserve their use of either server. Suzy Strickler can give them access and explain how to use the calendar to make reservations.
Server Best Practices (Reservation Calendar)
The Bioinformatics Consulting Station, located in the Resource Center, can now be reserved using the Outlook calendar. There are blocks of time allocated specifically for bioinformatics consulting, but other times are available for your use as well.
You may reserve the space for small group meetings or use it as you formerly used the public windows computer. Available software includes Office, Creative Suite, and DNA Star.
You can invite the meeting space to a meeting on your own calendar: btibioinformatic.
You can view the calendar directly in Outlook (these instructions are for Windows Outlook, Mac version may be slightly different):
In the Navigation Pane click Calendar. On the Home tab of the ribbon, in the Manage Calendar section, click Open Calendar, then select Open Shared Calendar. In the small Open a Shared Calendar dialog box, click Name.
In the Select Name dialog box, search by typing the btibioinformatic, then click Go.
Select the desired calendar in the resulting list, then click OK to close the Select Name dialog box.
Click OK to close the Open a Shared Calendar dialog box.
The bioinformatics calendar will now appear under Shared Calendars in your Navigation Pane. You can choose which calendars to have open using the checkboxes that appear next to each calendar’s line in your Navigation Pane.
If staff need help running analyses, or any other bioinformatics task, please contact Suzy Strickler of the BTI bioinformatics help desk or attend the BTI bioinformatics hour, which is held by Suzy every Wednesday from 1–2 p.m. in the Resource Center.
BTI Server Software
The following software is installed on the Boyce and William servers at Boyce Thompson Institute:
- DESeq and edgeR
- SOAP de novo
Contact Suzy Strickler if you need other software installed.
The following biological databases can be found on the Boyce and William servers at /data/. You can use these databases for analysis to reduce redundancy on the servers.
- nt and nr
- Swiss-Prot (curated database–high quality)
- TrEMBL (electronically annotated, not curated)
- To add: Tomato, Arabidopsis, Grape, Rice
Other publicly available databases not currently on BTI servers
- Genbank (SRA, pubmed)
- RepBase – repeats
- TAIR – Arabidopsis
- Solgenomics – Solanaceae and relatives
- Fei Lab Databases
- Phytozome – plant genomics resources.
If your lab frequently uses a database not currently available on the BTI servers, please contact Suzy Strickler so it can be added.