Orion(I own a total of 9 servers all running
CentOS) that I regularly administer and that run the workflows and the software I develop in collaboration with my colleagues as well as the most frequently used third-party software (400+ bioinformatics tools. Below is the university-wide usage (November 2015) of my cluster with brown boxes representing the research groups from College of Medical, Veterinary and Life Sciences, blue box representing the research group from College of Science & Engineering, along with emoticons for both PhD students and PostDocs:
GlobalView: A software for inferring multiple networks from time series data [Code]
RvLab(with collaborators at HCMR, Greece) makes use of
Rwhich is a statistical processing environment widely used by scientists working in many biodiversity related disciplines. It supports an integrated and optimized (in respect to computational speed-up and data manipulation) online
Renvironment. This vLab tackles common problems faced by
Rusers, such as severe computational power deficit. Many of the routines operating under the R environment, such as the calculation of several biodiversity indices and the running of the multivariate analyses, are often of high computational demand and cannot deliver a result when the respective datasets are in the form of large matrices.
CONCOCT: A software for binning metagenomic contigs with coverage and composition.
CViewer(Ongoing project; Designed by Orges Koci): Java-based visualisation tool for CONCOCT pipeline.
pyTag(Ongoing project; Designed by Orges Koci): A tool for identification and analyses of ontological terms in application area specific literature surveys.
AmpliPyth(Ongoing project; Designed by David Meltzer): Python-based pipeline that processes metagenomic amplicons (16S rRNA/18S rRNA and Fungal ITS) and generates an HTML report.
SNPCallPHYLO(Ongoing project; Designed by Dr Cosmika Goswami): Python-based SNPs calling pipeline that processes whole genome shotgun sequencing data from single genome isolates and generates an HTML report.
NMGS: A software for fitting the Unified Neutral Theory of Biodiversity with Hierarchical Dirichlet Process.
AMPLImock: A python based pipeline for analyzing 16s rRNA amplicons generated from mock communities [Code, Usage]
bashbased pipeline for generating taxonomic profiles for Illumina paired-end reads using
METAmock: A python based pipeline for analyzing Whole-Genome Shotgun sequences generated from mock communities [Code, Usage]
TAXAenv: A website useful for multivariate statistical analysis of microbial community structure (abundance tables) in an environmental context (metadata).
bashbased pipeline for generating taxonomic prifles using NCBI's Taxonomy.
CLUSThack: A python package that has an embarassingly-parallel (multithreaded + utilises streaming SIMD extensions) implemention for qgram-based edit distance measurement and is useful for hierarchical clustering of 16S rRNA sequences.
$ time ./hclust.py -f test.fasta -t 32
seqenv: A pipeline capable of annotating genetic sequences with Environmental Ontology.
clust_validity.R: This script takes a CSV file of N D-dimensional features, performs K-means or dp-means clustering and chooses the optimum number of clusters based on either of the implemented internal clustering validation indices. Additionally, if the csv file contains a column titled "True_Clusters" containing true clusters membership for each object, you can use it to validate clustering performance using several external clustering indices.
clust_validity.R(Tutorial, Reference slides (maths), Example datasets)
PHYLOmap: A software for drawing heatmaps with phylogenetic trees from metagenomic surveys based on Interactive Tree of Life (ITOL) API.
HEATcloud: Web-based interactive heatmap viewer (programmed using
jQuery) for abundance tables.
SUMMARIZEplot: Web-based interactive stacked barplot viewer (programmed using
D3) for abundance tables.
PHYLObar: Web-based interactive viewer (programmed using
D3) for trees in Newick format.
GraphicalLasso.tar.gz: Generates network of associations between OTUs as a DOT file which can then be visualised in
GNUparallel: For an Illumina dataset with 6 million reads,
blastn_parallel.shtook 2.5 minutes on 45 cores as compared to
blastn.shwhich took 86 minutes.
extract_clust_seqs_fasta.plis an extension of
Typical.pland can give the most abundant sequence, consensus sequence, first sequence, and the longest sequence of each cluster as representative OTU.
Rscript to iteratively remove colinear variables by calculating step-wise Variance Inflation Factor (VIF) of terms (columns) in a CSV file.
convIDs.pl: This script takes a (TAB/COMMA) delimited file and converts words in a particular column to those provided by a COMMA delimited IDs list.
Rscript takes two frequency tables in CSV format and collates them together by either taking union or intersection of columns. Furthermore it inserts "F1_" and "F2_" as prefixes to rownames of both CSV files, respectively.
collateResults.pl: This script is useful for combining CSV files generated by
AMPLICONprocessingor any software that produces two-column CSV files without header information. It takes as an input the path to a main folder where subfolders contain CSV files, each matching a particular pattern in their names.
collateGCMSResults.pl: This script is useful for collating data generated from GC-MS machines.
V Svolos, R Hansen, UZ Ijaz, C Quince, D Watson, A Alghamdi, A Brejnrod, C Ansalone, S Milling, D Gaya, R Russell, and K Gerasimidis
DOP008 Dietary manipulation of the healthy human and colitic murine gut microbiome by CD-TREAT diet and exclusive enteral nutrition; a proof of concept study
Journal of Crohn's and Colitis, 11 (suppl 1): S29-S30, 2017. DOI: 10.1093/ecco-jcc/jjx002.045
UZ Ijaz, C Quince, L Hanske, N Loman, ST Calus, M Bertz, CA Edwards, DR Gaya, R Hansen, P McGrogan, RK Russell, and K Gerasimidis
The microbial 'dysbiosis' of Crohn's disease patients does not occur in their unaffected, genetically linked kindred
PLoS ONE, 12(2): e0172605, 2017. DOI: 10.1371/journal.pone.0172605
S Connelly, SG Shin, RJ Dillon, UZ Ijaz, C Quince, WT Sloan, and G Collins
Bioreactor scalability: laboratory-scale idealisation influences performance, ecology and community physiology in expanded granular sludge bed bioreactors
Frontiers in Microbiology, accepted for publication (2017).
J De Vrieze, ME Christiaens, D Walraedt, A Devooght, UZ Ijaz, and N Boon
Microbial community redundancy in anaerobic digestion drives process recovery after salinity exposure
Water Research, 111:109-117, 2017. DOI:10.1016/j.watres.2016.12.042
C Pedersen, P Hinton, E Gallagher, F Horton, R Ellis, UZ Ijaz, H Wu, E Jaiyeola, O Diribe, GR Gibson, T Duparc, PD Cani, J Wright, D Russell-Jones, RL Ragione, and MD Robertson
Galacto-Oligosaccharide has no Effect on Glucose Tolerance, inflammatory Markers or Intestinal Permeability in well-controlled Type 2 Diabetes
Proceedings of the Nutrition Society, 75(OCE3), 2016. DOI:10.1017/S0029665116001191
C Pedersen, E Gallagher, F Horton, RJ Ellis, UZ Ijaz, H Wu, E Jaiyeola, O Diribe, T Duparc, PD Cani, GR Gibson, P Hinton, J Wright, D Russell-Jones, R La Ragione, and MD Robertson
Host-microbiome interactions in human type 2 diabetes following prebiotic dietary fibre (galacto-oligosaccharide) intake
British Journal of Nutrition, 116(11):1869-1877, 2016. DOI:10.1017/S0007114516004086
JL Ray, J Althammer, KS Skaar, P Simonelli, A Larsen, D Stoecker, A Sazhin, UZ Ijaz, C Quince, JC Nejstgaard, M Frischer, G Pohnert, and C Troedsson
Metabarcoding and metabolome analysis of copepod grazing reveals feeding preference and linkage to metabolite classes in dynamic microbial plankton communities
Molecular Ecology, 2016. DOI:10.1111/mec.13844
L Sinclair*, UZ Ijaz*, LJ Jensen, M Coolen, C Gubry-Rangin, A Chronakova, A Oulas, C Pavloudi, J Schnetzer, A Weimann, AZ Ijaz, A Eiler, C Quince, and E Pafilis
Seqenv: linking microbes to environments through text mining
PeerJ, 4:e2690, 2016. DOI:10.7717/peerj.2690
*Joint first authors
K Gerasimidis, M Bertz, C Quince, K Brunner, A Bruce, E Combet, ST Calus, N Loman, and UZ Ijaz
The effect of DNA extraction methodology on gut microbiota research applications
BMC Research Notes, 9:365, 2016. DOI:10.1186/s13104-016-2171-7
V Svolos*, R Hansen, K Hughes, UZ Ijaz, C Quince, D Gaya, R Russell, and K Gerasimidis
The impact of 'Crohn's Disease-TReatment-with-EATing' diet (CD-TREAT diet) and exclusive enteral nutrition on healthy gut bacteria metabolism
Journal of Crohn's and Colitis, 10(suppl 1):S14-S15, 2016. DOI:10.1093/ecco-jcc/jjw019.017
*Winner of Best investigator-initiated study (IIS) Award at the 11th Congress of ECCO
C Varsos, T Patkos, A Oulas, C Pavloudi, A Gougousis, UZ Ijaz, I Filiopoulou, N Pattakos, EV Berghe, A Fernandez-Guerra, S Faulwetter, E Chatzinikolaou, E Pafilis, C Beikiari, M Doerr, and C Arvantidis
Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)
Biodiversity Data Journal, 4:e8357, 2016. DOI:10.3897/BDJ.4.e8357
N De Souza, G Douce, C Goswami, UZ Ijaz, D Brown, J Coia, P Donnan, C Wiuff, P Davey, M Bennie, J Lindstrom, and C Marwick
Genetic relatedness among clinical Clostridium difficile strains in one Scottish region
In 26th ECCMID, Amsterdam, Netherlands, 9-12 April, 2016
QM Bautista-do los Santos, JL Schroeder, MC Sevillano-Rivera, R Sungthong, UZ Ijaz, WT Sloan, and AJ Pinto
Microbial communities in full-scale drinking water distribution systems - A meta-analysis*
Environmental Science: Water Research & Technology, 2:631-644, 2016. DOI:10.1039/C6EW00030D
*Features in Environmental Science: Water Research & Technology 2016 Most Downloaded Articles
K Gerasimidis, UZ Ijaz, C Edwards, RK Russell, C Quince, and R Hansen
Response to Kaakoush et al.
American Journal of Gastroenterology, 111(7):1033-1034, 2016.
M Schirmer, R D'Amore, UZ Ijaz, N Hall, and C Quince
Illumina error profiles: Resolving fine-scale variation in metagenomic sequencing
BMC Bioinformatics, 17:125, 2016. DOI:10.1186/s12859-016-0976-y
AJ Pinto, DN Marcus, UZ Ijaz, QM Bautista-de los Santos, GJ Dick, and L Raskin
Metagenomic evidence for the presence of Comammox Nitrospira-like bacteria in drinking water system
mSphere, 1 (1): e00054-15, 2015. DOI:10.1128/mSphere.00054-15
M Castelino, S Eyre, M Tutino, J Moat, P Martin, UZ Ijaz, C Quince, P Ho, M Upton, A Barton
Bacterial Skin Microbiome in Psoriatic Arthritis - Pilot Data from Psoriatic Plaques on Dry Skin Sites from Patients with Psoriasis (PsC) and Psoriatic Arthritis (PsA) [abstract]
Arthritis & Rheumatology, 67 (suppl 10), 2015. DOI:10.1002/art.39448
R D'Amore*, UZ Ijaz*, M Schirmer, J Kenny, R Gregory, AC Darby, M Shakya, M Podar, C Quince, and N Hall
A comprehensive benchmarking study of next-generation sequencing platforms for 16S rRNA community profiling
BMC Genomics, 17:55, 2016. DOI:10.1186/s12864-015-2194-9
*Joint first authors
B Torondel, JHJ Ensink, O Gundogdu, UZ Ijaz, J Parkhill, F Abdelahi, V-A Nguyen, S Sudgen, W Gibson, AW Walker, and C Quince.
Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines
Microbial Biotechnology, 9(2):209-223, 2016. DOI:10.1111/1751-7915.12334
E Pafilis, S Frankfield, L Fanini, S Faulwetter, C Pavloudi, J Schnetzer, A Vasileiadou, UZ Ijaz, C Arvanitidis, R Stevenson, and LJ Jensens
Identification of Environmental Ontology terms in text and the annotation of the Encyclopedia of Life
In TDWG 2014 Annual Conference, Jönköping, Sweden, October 27-31, 2014.
C Quince*, UZ Ijaz*, N Loman, AM Eren, D Saulnier, J Russell, SJ Haig, ST Calus, J Quick, A Barclay, M Bertz, M Blaut, R Hansen, P McGrogan, RK Russell, C Edwards, and K Gerasimidis
Extensive modulation of the fecal metagenome in children with Crohn's disease during exclusive enteral nutrition
American Journal of Gastroenterology, 110:1718-1729, 2015. DOI:10.1038/ajg.2015.357
*Joint first authors
C Goswami, UZ Ijaz, DJ Brown, CA Marwick, C Wiuff, A Banks, JE Coia, and GR Douce
Understanding molecular epidemiology of Clostridum Difficile in Scotland
In 5th International Clostridum Difficile Symposium, May 19-21, 2015, Bled, Slovenia.
MJ Khan, C Quince, V S, UZ Ijaz, N Loman, ST Calus, J Quick, SJ Haig, MG Shaikh, CA Edwards, and K Gerasimidis
A detailed analysis of the gut microbial diversity and metabolic activity in children with obesity of different aetiology and lean controls
Proceedings of the Nutrition Society, 74(OCE1):E75, 2015.
M Castelino, S Eyre, J Moat, G Fox, P Martin, UZ Ijaz, C Quince, P Ho, M Upton, and A Barton
The skin microbiome in psoriatic arthritis: methodology development and pilot data
Lancet, 385(Supplement 1):S27, 2015.
JM Couto, UZ Ijaz, VR Phoenix, M Schirmer, and WT Sloan
Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment
Current Microbiology,71(2), 296-302, 2015.
M Schirmer, UZ Ijaz, R D'Amore, N Hall, WT Sloan, and C Quince
Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform
Nucleic Acids Research, 2015.
D Savio, L Sinclair, UZ Ijaz, P Stadler, AP Blaschke, GH Reischer, G Bloeschl, RL Mach, AKT Kirschner, AH Farnleitner, and A Eiler
Bacterial diversity along a 2 600 km river continuum
Environmental Microbiology. doi: 10.1111/1462-2920.12886, 2015.
K Harris, TL Parsons, UZ Ijaz, L Lahti, I Holmes, and C Quince
Linking statistical and ecological theory: Hubbell's unified neutral theory of biodiversity as a hierarchical Dirichlet process
Proceedings of the IEEE, pp. 1-14 (Early Online Publication)
J Alneberg, BS Bjarnason, I de Bruijn, M Schirmer, J Quick, UZ Ijaz, L Lahti, NJ Loman, AF Andersson, and C Quince
Binning metagenomic contigs by coverage and composition.
Nature Methods, 2014.
K Gerasimidis, N Loman, J Quick, ST Calus, UZ Ijaz, P McGrogan, CA Edwards, C Quince, and R. K. Russell
O-05: Metagenomic analysis of the gut microbiome during a course of Exclusive Enteral Nutrition (EEN) provides novel insights on mechanism of EEN action
Journal of Crohn's and Colitis, 8(Supplement 2):S393-S394, 2014.
RJ Housden, GM Treece, RW Prager, and AH Gee.
Multi-directional scattering models for 3-dimensional ultrasound imaging
Journal of Ultrasound in Medicine, 32(4):699-714, April 2013.
E Dyer, UZ Ijaz, RJ Housden,
RW Prager, AH Gee, and GM Treece.
A clinical system for three-dimensional extended field of view ultrasound
British Journal of Radiology, 85: e919-e924, October 2012. Relevant Software:
UZ Ijaz, RW Prager, AH Gee, and GM Treece
A study of similarity measures for in vivo 3D ultrasound volume registration
Acoustical Imaging, 30:315-323, 2011.
UZ Ijaz, RW Prager, AH Gee, and GM Treece
Particle swarm optimization for in vivo 3D ultrasound volume registration
Acoustical Imaging, 30:345-354, 2011.
RW Prager, AH Gee, and GM Treece
Optimisation strategies for ultrasound volume registration
Measurement Science and Technology, 21(8): 085803 (17pp), July 2010.
RW Prager, UZ Ijaz , AH Gee, and GM Treece
Three-dimensional ultrasound imaging
Proceedings of the Institution of Mechanical Engineers Part H-Journal of Engineering in Medicine, 224(2):193-223, 2010.
AK Khambampati, UZ Ijaz, JS Lee, S Kim, and KY Kim
Phase boundary estimation in electrical impedance tomography using Hooke and Jeeves pattern search method
Measurement Science and Technology, 21(3):035501 (13pp), March 2010.
UZ Ijaz, AK Khambampati, JS Lee, S Kim,
and KY Kim
Nonstationary phase boundary estimation in electrical impedance tomography using unscented Kalman filter
Journal of Computational Physics , 227(15):7089.7112, July 2008.
UZ Ijaz, AK Khambampati, MC Kim, S Kim, JS Lee, and KY Kim
Particle swarm optimization technique for elliptic region boundary estimation in electrical impedance tomography
AIP Conference Proceedings, 914:896-901, 2007.
UZ Ijaz, AK Khambampati, JS Lee, KY Kim, MC Kim, and S Kim
Electrical resistance imaging of two-phase flow through rod bundles
AIP Conference Proceedings, 914:844-849, 2007.
BS Kim, UZ Ijaz, JH Kim, MC Kim, S Kim, and KY Kim
Nonstationary phase boundary estimation in electrical impedance tomography based on the interacting multiple model scheme
Measurement Science and Technology, 18(1):62-70, January 2007.
Dynamic phase boundary estimation in electrical impedance tomography
PhD thesis, Cheju National University, Korea, December 2007.
AK Khambampati, A Rashid, UZ Ijaz, S Kim, M Soleimani, and KY Kim
Unscented Kalman filter approach to tracking a moving interfacial boundary in sedimentation process using three-dimensional electrical impedance tomography
Philosophical Transactions of The Royal Society A - Mathematical Physical and Engineering Sciences, 367:3095-3120, August 2009.
SI Chung, AK Khambampati, KY Kim, and S Kim
Electrical resistance imaging of time-varying interface in stratified flows using unscented Kalman filter
Measurement Science and Technology, 19(6) 065501 (11pp), June 2008.
S Kim, UZ Ijaz, AK Khambampati, KY Kim, MC Kim, and
Moving interfacial boundary estimation in stratified flows of two immiscible liquids using electrical resistance tomography
Measurement Science and Technology, 18(5):1257-1269, May 2007.
JH Kim, BC Kang, SH Lee, BY Choi, MC Kim, BS Kim, UZ Ijaz, KY Kim, and S Kim
Phase boundary estimation in electrical resistance tomography with weighted multi-layered neural networks and front point approach
Measurement Science and Technology, 17(10):2731-2739, October 2006.
BS Kim, TJ Kao, AK Khambampati, S Kim, MC Kim, JC Newell, D Isaacson,
and KY Kim
Mammography phantom studies using 3D electrical impedance tomography with numerical forward solver
In FBIT 2007:379-383.
UZ Ijaz, JH Kim, AK Khambampati, MC Kim,
S Kim, and KY Kim
Concentration distribution estimation of fluid through electrical impedance tomography based on interacting multiple model scheme
Flow Measurement and Instrumentation, 18(1):47-56, March 2007.
JH Kim, BY Choi, UZ Ijaz, BS Kim, S Kim, and KY Kim
Directional algebraic reconstruction technique for electrical impedance tomography
Journal of The Korean Physical Society, 54(4):1439-1447, April 2009.
YS Kim, SH Lee, UZ Ijaz, KY Kim, and BY Choi
Sensitivity map generation in electrical capacitance tomography using mixed normalization models
Measurement Science and Technology, 18(7):2092-2102, July 2007.
FA Khan, UZ Ijaz, KY Kim, MJ Kang, and WC Song
Policy-based management in ad hoc network using geographic routing
Lecture Notes in Computer Science, 3961:237-246, 2006.
S Kim, UZ Ijaz, AK Khambampati, KY Kim, and MC Kim
Effect of Current Injection Patterns on Dynamic Electrical Resistance Imaging for Fast Transient Processes
In 5th IEEE Conference on Sensors, 2006.
UZ Ijaz, JH Kim, MC Kim, S Kim, JW Park,
and KY Kim
Nondestructive dynamic process monitoring using electrical capacitance tomography
Key Engineering Materials, 321-323(2):1671-1674, 2006.
AK Khambampati, MC Kim, S Kim, and KY Kim
Estimation of time-dependent heat flux and measurement bias in two-dimensional heat conduction problems
International Journal of Heat and Mass Transfer, 50(21-22):4117-4130, October 2007.
SU Chaudhary, SM Ahn, BH Lee, and KY Kim
Computational strategies for protein quantitation in 2D electrophoresis gel image processor for Matlab
In FBIT 2007: 129-134.
UZ Ijaz, SU Chaudhary, SM Ahn, BH Lee, and
2D electrophoresis gel image processor for Matlab
In ICHIT 2006, Jeju, Korea, November 9-11, 2006.
Professor William Sloan
Dr Caroline Gauchotte-Lindsay
Dr Jillian Couto
Dr Cindy Smith
|Infrastructure & Environment|
|Professor Barbara Mable
Professor Neil Metcalfe
Dr Jan Lindstrom
|Institute of Biodiversity, Animal Health and Comparative Medicine|
|Dr Christina Cobbold||School of Mathematics and Statistics|
|Dr Huabing Yin||Biomedical Engineering|
|Dr Martin Llewellyn||School of Life Sciences|
|Dr Gillian Douce
Dr Simon Milling
Dr Andrew Roe
|Institute of Infection, Immunity and Inflammation|
|Professor Christine Edwards
Dr Konstantinos Gerasimidis
|School of Medicine (Human Nutrition)|
|Dr Jaime Toney
Professor Maggie Cusack
|School of Geographical and Earth Sciences|
|Dr Ameet Pinto|
Dr Richard Russell
Dr Richard Hansen
Dr Daniel Gaya
Dr Seung Gu Shin
Dr Juhee Shin
|Dr Douglas Morrison|
Scottish Salmonella, Shigella and
Clostridium difficile Reference Laboratory (SSSCdRL)
Professor John E Coia
Dr Derek Brown
Dr Charis Marwick
Professor Peter T Donnan
Dr Phillip McGinnity
Dr Thomas Reed
|Dr Christopher Quince|
|Dr Leo Lahti|
Dr Gavin Collin
Dr Florence Abram
Professor Anne Barton
Dr Madhura Castelino
Dr Belen Torondel
Dr Ozan Gundogdu
|Dr Alan Walker|
|Professor Mark Pritchard|
|Professor Neil Hall|
|Dr Jessica Louise Ray|
|Professor Lars Juhl Jensen|
|Dr Evangelos Pafilis|
|Dr. R.J.J.H. (Rob) van Son|