FACILITIES AND OTHER RESOURCE – The Covenant University Bioinformatics Research, Covenant University (CUBRe), Ota, Nigeria

1. Environment – Contribution to Success

   Covenant University is a leading Private University in Nigeria, having all her courses fully accredited by the National Universities Commission (NUC), and is ranked and listed among the first 100 Universities in Africa. The University is blessed with a serene environment and infrastructures that can aid quality research output. Recently, the Covenant University Bioinformatics Research (CUBRe) in a consortium with project title “H3ABioNet: a sustainable African Bioinformatics Network for H3Africa” won a research award (Grant Number: 1U41HG006941-01) from the NIH/NHGRI. Covenant University is the only Nigerian Institution in this consortium. All our research efforts in bioinformatics have been recently reconsolidated in the establishment of a unit on bioinformatics research, namely Covenant University Bioinformatics Research (CUBRe (http://cubre.covenantuniversity.edu.ng)). Emphasizing our maturity, CUBRe will host the H3ABioNet “Masters” Bioinformatics Workshop between 21st April to 26th, May 2014. The Management of CU is further building strong on this by a recent initiative to endow a research chair in the area of bioinformatics and biotechnology. Please see >>>
   Our proposed research is centered on two research projects (Projects II & III) which we are currently pursuing under the CODE MALARIA projects, (please see >>), namely “Computationally aided identification and validation of evolution-proof insecticidal targets in A. gambiae mosquito” and “Malaria control mathematical modeling”.

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2. Facilities:

   These are divided into dry and wet laboratories

   • Dry Laboratory

     • High Performance Computing Facility:

       • Slave
         4 Dell PowerEdge R410 Server: 2 x Intel Xeon E5507, 4C, 2.26GHz, 4M Cache, 4.80GT/s, 80W TDP, Turbo, HT, DDR3-800MHz/2x 300GB, SAS 6Gbps, 3.5-in, 15K RPM Hard Drive (Hot Plug)/ 24GB Memory for 2 CPUs, DDR3, 1333MHz (6x4GB Dual Ranked RDIMMs)/ 16X DVD+/-RW Drive SATA with SATA cable/ C7 Hot-Swap.
       • Master
         PowerEdge C6145 Chassis with 1 System Board v2 and Expander Backplane, support for up to 12x 3.5″ HDDs
         Components: 4x AMD Opteron 6386SE (2.8GHz, 16C, 16M L2/16M L3 Cache, Turbo CORE, 140W TDP), DDR3-1600MHz (ZR), 1 256GB Memory for 4CPU (16x16GB Dual Rank LV RDIMMs) 1333MHz (ZR), 2 500GB, SATA, 3.5-in, 7.2K RPM Hard Drive (Hot-plug) (ZR), 5 2TB, SATA, 3.5-in, 7.2K RPM Hard Drive (Hot-plug) (ZR), 1 Redundant Power Supply, 1400W (2 PSUs included) – 1 or 2-Node Configs (ZR), 2 Power Cord, 2M, C13 to C14, PDU Style, 12 Amps (ZR), 1 C6000/C6145 Static Rack Rails, Tool-less (ZR), 1 C11 – 3.5″ 1-Node 115W/140W CPUs (Mezz) with LSI2008 SAS/SATA Mezz, 1-8 SAS/SATA HDs

     • High Performance Computing Facility (Extension)

       Recently, we ungraded the facility above with system of the following specification: PowerEdge C6145 Chassis with 1 System Board v2. Expander Backplane, support for up to 12x 3.5″ HDDs. Components: 4x AMD Opteron 6386SE (2.8GHz, 16C, 16M L2/16M L3 Cache, Turbo CORE, 140W TDP), DDR3-1600MHz (ZR), 1 256GB Memory for 4CPU (16x16GB Dual Rank LV RDIMMs) 1333MHz (ZR), 2 500GB, SATA, 3.5-in, 7.2K RPM Hard Drive (Hot-plug) (ZR), 5 2TB, SATA, 3.5-in, 7.2K RPM Hard Drive (Hot-plug) (ZR), 1 Redundant Power Supply, 1400W (2 PSUs included) – 1 or 2-Node
       Configs (ZR), 2 Power Cord, 2M, C13 to C14, PDU Style, 12 Amps (ZR), 1 C6000/C6145 Static Rack Rails, Tool-less (ZR), 1 C11 – 3.5″ 1-Node 115W/140W CPUs (Mezz) with LSI2008 SAS/SATA Mezz, 1-8 SAS/SATA HDs, (No RAID) (ZR), Software: Performance Optimized BIOS Setting

     • Other resources available:

       40 specified PCs for research and training are located in the Department of Computer and Information Sciences Postgraduate lab. Two other labs also exist with 250 and 100 general PCs purely for training. The one with 100 general PCs is located in the University Library, while the other is located in the College of Science and Technology, which houses the Department of Computer and Information Sciences. All systems have access to high-speed connections to the University campus’ wired and wireless networks and internet.

     • CUBRe Staff Computer:

       The main Africa site PI/PD for this application is the PI/PD for the CU NIH H3AbioNet node hosted by CUBRe. The PI/PD has a thinkpad laptop and a desktop with both Windows and Linux OS.
       Office: The PI has a personal office and also other offices for CUBRe’s Research Scientists.

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   • Wet lab

     Several laboratories exist at CUBRe to enable us carry out the biological experiments and analysis anticipated in this application. You can check out free research papers . Relevant equipment to this project (at these laboratories) include:

     S/N	Equipment	Uses
     1	High Performance Liquid Chromatography system	Separation and quantification of metabolites and bioactives
     2	Refrigerators and Freezers	Storage of biological materials
     3	Centrifuges	Extraction of nucleic acids and protein
     4	Thermal cycler	Multiplication/amplification of nucleic acid
     5	Electrophoresis apparatuses	Separation of nucleic acids and proteins
     6	Blotting apparatuses	Transfer of nucleic acids and proteins unto membranes for identification and quantification
     7	Gel documentation system	Visualization of nucleic acids and proteins in electrophoresis gel
     8	Co2 incubator	Culturing/growing tissue for in vitro experiments
     9	Spectrophotometer	Quantification of metabolite and assay of enzyme activity.
     10	Nanodrop	Quantification of nucleic acids after extraction

   • S/N	List of Equipment in FEDGEN Lab
     1	Testbed: Servers (MaaS), Controller node, compute node. Dell PowerEdge R740 8x SFF 1U server 16GB RAM E5-2620, 300GB X 2 SAS, 1TB X 2 SAS with rack mount.
     2	Front End Server: Supermicro Complete Integrated Server - 825TQC-R740LPB 2U Chassis with 8 Hot Swap Drive Bays & 2 internal Fixed Drive bays - Redundant 740Watt Power Supply
     3	Flash Storage: CyberStore 316S - SAS3 12Gb/s - with Redundant 920Watt Hot Swap Power SuppliesUltra-Performance SAS3 12Gb/s Storage Chassis - 16x 3.5 Drives
     4	Supermicro Complete Integrated Server 825TQC-R740LPB 2U Chassis with 8 Hot Swap Drive Bays & 2 Internal Fixed Drive bays - Redundant 740-Watt Power Supply
     5	GPU Computing:Chassis ASUS ESC4000-G4 Server, Redundant 1600W Power Supply Processor 2x Intel Xeon Silver 4210 Processor - 10 Cores, 2.20GHz, 13.75MB Cache (85Watt) Memory 8x 128GB 2933MHz DDR4 ECC Registered DIMM Module Hard Drive 2x 960GB Intel SSD S4510 Data Centre SERIES 2.5IN SATA3 TLC RAID Controller Card LSI MegaRAID 9341-8i 12Gb/s SAS/SATA RAID Controller, No Cache (No RAID 6 / 60) Nvidia Tesla and AMD FirePro GPU Compute Cards 4x NVIDIA RTX 3090 Blower Edition GPU Card, Gen4, 24GB GDDR6, 10496 Cores PCI Express Expansion Intel X710-DA2 - Dual-Port 700 Series Network Adapter SFP+ 10/1GbE
     6	Windows 11 Pro Windows 11 Pro ZBook Fury 17 G8with Intel® Core™ i9-11900H processor (2.5 GHz, up to 4.9 GHz with Turbo Boost, 24 MB cache, 8 core) + Intel® UHD Graphics + WWAN available (46Q01AV) 17.3" diagonal FHD LED UWVA Anti-Glare for HD Webcam Ambient Light Sensor (1920x1080) 300 Nits
     7	Epson EB-W51 - 3LCD projector- portable - 4000 lumens (white) - 4000 lumens (colour) - WXGA (1280 x 800) - 16:10 - 720p
     8	2019 Apple MacBook Pro (16-inch, 16GB RAM, 1TB Storage, 2.3GHz Ninth-generation 8-Core Intel Core i9 Processor) FEATURES Ninth-generation 8-Core Intel Core i9 Processor Stunning 16-inch Retina Display with True Tone technology Touch Bar and Touch ID AMD Radeon Pro 5500M Graphics with GDDR6 memory Ultrafast SSD Intel UHD Graphics 630 Six-speaker system with force-cancelling woofers Four Thunderbolt 3 (USB-C) ports Up to 11 hours of battery life 802.11ac Wi-Fi Space Gray

   • Molecular Biology Laboratory: The molecular laboratory is located at the 1st floor, left wing of CUCRID Building, Covenant University, KM. 10 Idiroko Road, Canaan Land, Ota, Ogun State, Nigeria.

     S/N	List of Equipment in Molecular Biology Lab	Uses
     1	Refrigerated Incubator Shaker	Culturing/growing of tissue
     2	Refrigerators and Freezers	Storage of biological materials
     3	Centrifuges	Extraction of nucleic acids and protein
     4	Mastercycler	Multiplication/amplification of nucleic acid
     5	Electrophoresis apparatuses	Separation of nucleic acids and proteins
     6	Sonicator	Breaking of cells.
     7	Gel documentation system	Visualization of nucleic acids and proteins in electrophoresis gel
     8	CO2 incubator	Culturing/growing tissue for in vitro experiments
     9	Refrigerated Centrifuge	Separation of mixtures
     10	Water purification system	Production of distilled and RNA
     11	pH meter	Measuring the level of acid and base of a solution
     12	Autoclave	For sterilization
     13	Weighing balance	Determination of samples weight
     14	Heating mantle	Warming of samples
     15	Filtration vacuum pump	For filtration of samples
     16	Roto – Therm	For mixing of samples

   • Organic Chemistry Laboratory:The organic chemistry laboratory is located at the 1st floor, left wing of CUCRID Building, Covenant University, KM. 10 Idiroko Road, Canaan Land, Ota, Ogun State, Nigeria.

     S/N	List of Equipment in Organic Chemistry Lab	Uses
     1	Benchtop nuclear magnetic resonance (NMR) spectrometer (60MHz)	Used in chemical synthesis to monitor reaction, quality assurance/quality control of experiments and structural elucidation of synthesized compounds
     2	Biobase Water bath	Heat source for flammable chemicals, to facilitate chemical reactions, to heat up chemical reagents and increase the solubility of some insoluble substances
     3	Stainless steel water distiller	Purify water using distillation process
     4	Stuart Digital melting point apparatus	Determine the temperature at which a sample melt
     5	Stuart Magnetic stirrer hotplate	Conduct biological and chemical reaction
     6	Biobase Heating mantle	Apply heat to chemical reactions
     7	IKA Rotary evaporator	Sample concentration, crystallization, drying, separation, and solvent recovery in addition to the continuous distillation of volatile solvents
     8	Esco Laboratory Fume Hood	Protection against chemical spills, runaway reactions and fires by acting as a physical barrier.

   • In vitro LaboratoryThe in vitro laboratory is located at the 4th floor, right wing, CUCRID Building, Covenant University, KM. 10 Idiroko Road, Canaan Land, Ota, Ogun State, Nigeria.

     S/N	List of Equipment in In vitro Lab	Uses
     1	Hematocrit Centrifuge	Determination of volume fractions of erythrocytes (red blood cells) in blood and separation of micro volumes of blood and solutions
     2	Autoclave, STEAM Sterilizer. Stainless Steel, 20Litres	For sterilization
     3	Colony Counter	For counting parasites
     4	pH Meter	Measures hydrogen-ion activity (acidity or alkalinity) in solution
     5	Water Bath	Heat samples in the lab.
     6	Analytical Weighing Balance	Determination of samples weight
     7	Nuebaeur Chamber	Count cells in a biological fluid by observing them, through microscope, on a calibrated grid
     8	Clock/Timer	For measuring specific time intervals
     9	Light Microscope (Binocular for Research)	Used to provide information about the activity of cells and to look at very small structures such as nanostructures
     10	Staining Trough	Used to stain slides
     11	Hand Held Aspirator Pump	Dependable source of moderate vacuum in the laboratory
     12	4°C Fridge	Storage of biological materials
     13	Freezer -20 300Litres.	Storage of biological materials
     14	Biological Safety Cabinet Class II	Handling pathogenic biological samples or for applications that require a sterile work zone.
     15	ESCO Vertical Laminar flow ACB-4AI	Useful when product protection from contaminants is required
     16	Microscope Stereo Microscope with camera. Amscope, USA.	Provide low-magnification views of three-dimensional specimens

   • Cancer Genomics Laboratory: The FEDGEN laboratory is located at the 4th floor, right wing, CUCRID Building, Covenant University, KM. 10 Idiroko Road, Canaan Land, Ota, Ogun State, Nigeria.

     S/N	List of Equipment in Cancer Genomics Lab
     1	Agilent 450 Tape Station with full Accessories
     2	MiSeq System and Illumina Sequential
     3	Biosan Component Equipment & Accessories

FACILITIES AND OTHER RESOURCE – INTERNATIONAL CENTER OF EXCELLENCE IN RESEARCH, UNIVERSITY OF BAMAKO

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1. Environment – Contribution to Success

   The International Center of Excellence in Research (ICER) was created in 2002 through a cooperative agreement between the National Institute of Allergy and Infectious Diseases (NIAID) of the National Institutes of Health (NIH) and University of Bamako. The Center is a the result of long term research collaboration between Mali and NIH initiated in 1989 with the creation of the Malaria Research and Training Center (MRTC) with support from other partners including WHO, USAID and the International Atomic Energy Agency (IAEA). The ICER regroup 3 mains programs: the MRTC vaccine development program, the MRTC-Entomology and other vector born diseases programs and the HIV/AIDS/TB program (named SEREFO).
   The ICER was initiated by the NIAID DIR to recognize a select group of overseas research facilities and make them part of the regularized budget process of the Institute.
   The goal of the Mali ICER is to partner with in-country scientists to address major endemic diseases and foster research in areas such as malaria, HIV and tuberculosis. The ICER program is designed to build sustainable research capacity in regions with a high infectious disease burden. The scientific priorities of the ICER now encompass research on malaria pathogenesis; testing of candidate malaria vaccines; clinical research on filariasis, leishmaniasis; and HIV/TB co-infection. The Mali ICER currently provides in-country support for state-of-the-art laboratories at the University of Bamako and laboratory field sites in the villages of Bancoumana, Doneguebougou and Bandiagara on the Dogon Plateau.

2. Personal Resources and Training at the Mali-ICER

   Since the beginning of the program in Mali, the NIH has been cooperating in the training of Malian students, in Mali, in the US and at various Canadian and European research centers. More than 2 dozens of Ph.D and Master degree students, have been trained from US, UK, France, Italy, Canada, Belgium and other countries in Africa. The Center counts more than 30 scientists. A number of Malian graduate students at the ICER are working with mentors from US universities. For the past several Summers, Malian students have been enrolled in the Graduate Summer Institute of Epidemiology and Biostatistics at The Johns Hopkins University. Many of these are playing crucial roles in the vaccine testing effort. Several have completed training courses in bioethics in the US.
   The ICER has provided a unique venue for training scientists from the US and other countries. In 1998, the NIH launched a training program which provided training opportunities for undergraduate, graduate and medical students with emphasis on students from disadvantaged and under-represented backgrounds.
   The ICER continues to serve as a site for training. A fellow from the NIH Undergraduate Scholarship Program is currently in residence at the Center. Graduate students from US European and African universities are regularly in training at the Center.

3. Collaboration/Parnership at ICER-Mali:

   ICER collaborates with several Universities and Research Institution around the word. Though NIAID is the primary collaborator, the ICER competes with other research institutions for NIH extramural and other research grants. Collaboration with institutions include but not limited to Tulane University, Johns Hopkins University, Columbia University, U of Davis, University of Chicago, CDC, Harvard University, U of California at Davis and UCLA. In addition, the center provides technical support to National Disease Control Programs including (HIV/AIDS, Filariasis, Malaria, and TB control Programs). This support includes support to disease surveillance and training of control program staffs and health workers. The ICER also provides quality control of laboratories diagnosis to control programs. Support to control Programs also include operational research to guide Diseases Control Programs for evidence based-decision for treatment and prevention policy.

4. Research Facilities of the ICER-MALI

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   The following is a summary of laboratories in ICER program:
   The ICER encompass more than 15 laboratories specialized in basic Molecular biology, Genomics, Immunology, Epidemiology/GIS, Bioinformatics, Database management Center, a BSL-3 for TB and Clinical Research Laboratory. The Core facilities (managed by the ICER secretariat) include a Library/conference room (seats 60), Lunch room, Freezer room, Motor Pool, Storage facility (laboratory supplies), Guest House (can house up to 12 guests, with dining facility and computer room), Administrative offices, Communication network (dedicated satellite connection to the NIH)

   All the laboratories are fully equipped and house studies on the molecular biology and genomics. Equipment includes two dozen of PCR machines, three Real time PCR machines, 4 ELISA readers, ELISPOT and 2 DNA sequencing machines, and two in vitro parasite culture facilities are also available. 8 lab culture Class II Type A2 Biological Safety Cabinets, Eight inverted microscopes, One autoclave,Ten CO2 incubators, One fluorescent microscope, and Ten Freezers (both -20 and -80ºC).

   Other research resources:

   There is an animal facility with dozen of guinea pigs and mice to support research experiments. In addition; there are 2 insectaries with temperature, humidity and photoperiod control installed for the colonization and maintenance of mosquitoes of diverse genetics and molecular forms and mosquitoes membrane feeding experiments. The Mali ICER currently provides in-country support for state-of-the-art laboratories at the University of Bamako and laboratory field sites in the villages of Bancoumana, Doneguebougou and Bandiagara on the Dogon Plateau.

5. NIAID’s Research Support Office Development

   NIAID’s Research Support Office was developed in 2005 to develop an organized office structure which would unify all of DIR’s scientific management and administrative functions into one office. The Director of the office liaises with US and Malian government and NGO entities, the MSC, the intramural program, and extramural grantees.

6. NIAID’s Mali Service Center

   In 2004 a cooperative agreement was signed by the University of Bamako and NIAID on the development of a Mali Service Center (MSC), supported by NIAID, to assist University of Bamako in management of research funds from NIH and other international research funds with the idea of training and developing capacity for the MSC to be fully owned by Malians and the University of Bamako in the near future.

7. Information technology (IT/LAN)

   The center has more than 150 computers all connected to internets (for data management, for special training and for research staff), counts more than 50 desktops (Pentium 4 or more) computers and laptops in excellent condition. All computers are connected to an excellent and robust Internet connection (VSAT) through the NIH in Rockville, MD, USA. The Internet connection is provided through a satellite link with 128 KBps download/upload speeds. The network is routed through a server at mrtcbko.org, which also is the mail server. The computers and the networks are maintained by a team of 4 IT staffs. The servers include: a] two IBM xServer: Intel Xeon (2.0 GHz) processor, 1GB of RAM, 2 10,000 RPM SCSI hard drives (~20 GB or redundant storage currently available to users- can be expanded easily), b] two Compaq Proliant ML350 G2Tower Server (2) Pentium

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