Nov 28, 2022
Developments in PGC Mindanao Bioinformatics Digital Infrastructure
This protocol is a draft, published without a DOI.
- Paul Lorenzo A Gaite1,
- Dr Ritchie Mae T Gamot1
- 1PGC Mindanao
- PHA4GE Subgrant - Philippines
Protocol Citation: Paul Lorenzo A Gaite, Dr Ritchie Mae T Gamot 2022. Developments in PGC Mindanao Bioinformatics Digital Infrastructure. protocols.io https://protocols.io/view/developments-in-pgc-mindanao-bioinformatics-digita-cgh3tt8n
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: September 13, 2022
Last Modified: November 28, 2022
Protocol Integer ID: 69915
Keywords: developments in pgc mindanao bioinformatics digital infrastructure, pgc mindanao bioinformatics digital infrastructure, bioinformatics in pgc mindanao, bioinformatics analysis in the center, bioinformatics, bioinformatics analysis, pgc mindanao, underdeveloped digital infrastructure, fiber optic structured cabling for the internet connectivity, mindanao, additional peripherals such as ram expansion, fiber optic, workstation, hdd, ram expansion, storage capabilities in the center, storage capability, laboratory workstation, external hard drive, additional peripheral, internet connectivity, sequencer, ssd
Abstract
One of the major challenges that was identified for bioinformatics in PGC Mindanao was its underdeveloped digital infrastructure. Fortunately, there was an ample portion from the grant to fund the fiber optic structured cabling for the internet connectivity of the sequencers and laboratory workstations. The other portion of this allotment was used to upgrade the workstations used for bioinformatics analysis in the center and purchase additional peripherals such as RAM expansions and external hard drives (SSD and HDD) to expand memory and storage capabilities in the center, respectively.
Troubleshooting
Abstract/Introduction
One of the major challenges that was identified for bioinformatics in PGC Mindanao was its underdeveloped digital infrastructure. Fortunately, there was an ample portion from the grant to fund the fiber optic structured cabling for the internet connectivity of the sequencers and laboratory workstations. The other portion of this allotment was used to upgrade the workstations used for bioinformatics analysis in the center and purchase additional peripherals such as RAM expansions and external hard drives (SSD and HDD) to expand memory and storage capabilities in the center, respectively.
The protocol below shows the photos of the developments in the digital infrastructure of PGC Mindanao, starting from the installation of peripherals for the setup of structured cabling to establish internet connectivity in the sequencing and bioinformatics laboratories (Section 2), setup of cabling to establish internet connectivity of the sequencers (Section 3), testing of internet connectivity of sequencers and workstations (Section 4), and procurement of RAM expansions and external hard drives and installation of the RAM expansions (Section 5).
Structured cabling of Sequencing and Bioinformatics laboratories
This section shows the structured cabling of the sequencing and bioinformatics laboratories.
Figure 1 shows the cabling that connects the sequencing and bioinformatics laboratories to the university's internet system via one of the internet server rooms.
Figure 1. Connection to the university's internet system via server room
A data cabinet was set up near the bioinformatics laboratory, which connects it to the university's internet system. Figure 2 shows the installation of peripherals, such as the switch, within the data cabinet. Figure 3 shows the same data cabinet finished with the installed and functioning peripherals. Figure 4 shows the added wifi router inside the Bioinformatics laboratory to provide the wifi signal in the room as well as the workstations inside.
Figure 2. Installation of data cabinet (with peripherals) near Bioinformatics laboratory
Figure 3. Finished data cabinet (with functioning peripherals) near Bioinformatics laboratory
Figure 4. Added wifi router in the Bioinformatics laboratory
Another data cabinet was set up near the sequencing laboratory that connects it to the university's internet system, which is shown in Figure 5.
Figure 5. Finished data cabinet (with functioning peripherals) near sequencing laboratory
LAN cabling of sequencers
This section outlines the connection of the sequencers through the structured LAN cabling within the laboratory.
Figure 6 shows the structured LAN cabling of Illumina NextSeq 1000 and iSeq 1000 sequencers, and Figure 7 shows the structured cabling within the room to enable internet connection in the sequencers and within this area.
Figure 6. LAN Cabling of Illumina NextSeq 1000 and iSeq 100 sequencers
Figure 7. Structured cabling for the internet connectivity of the sequencers and computers in the laboratory
Testing of internet connectivity of sequencers and workstations
This section shows the tests performed to check the internet connectivity of the sequencers and workstations.
As mentioned in the previous sections the structured cabling in the sequencers and laboratory was put in place to enable internet connectivity, as evidenced in Figures 8-10.
Figure 8. Illumina iSeq 100 sequencer showing internet connection speed during a test
Figure 9. Computer within the laboratory showing internet connection speed during a test
Figure 10. Illumina NextSeq 1000 sequencer capable of accessing internet
Procurement of RAM expansions and external hard drives and installation of the RAM expansions
This section present the procurement of RAM expansions and external hard drives, and the installation of the procured RAM expansions.
Figures 11 and 12 show the procured external HDDs and RAM, which would augment current storage and memory needs. Figure 13 shows the installation of the RAM expansion to extend the memory of the current workstations.
Figure 11. Procured external HDDs and RAM expansion
Figure 12. Procured RAM expansion
Figure 13. RAM expansion being installed in one of the current bioinformatics workstations