Explore our community of HPC Projects and users, grouped by software titles or methods they are using in their research.

This mapping of software to research activity is generated by a word frequency analysis of the software and processes each active, published, HPC Project has submitted.

The wordcloud graphic above is a dynamic representation of the frequency analysis of the software used by our published HPC research projects.

We also maintain a directory of published projects which have used HPC facilities at Newcastle University.

Software Keyword	Frequency
used	44
simulations	14
modelling	11
new	4
into	6
support	10
technologies	2
including	30
project	47
gpu-accelerated	8
deep	13
learning	19
frameworks	4
pytorch	24
tensorflow	18
develop	2
train	2
reinforcement	3
models	15
energy	6
management	3
large-scale	14
data	51
processing	39
numerical	9
computations	4
performed	5
python	143
scientific	10
libraries	22
numpy	17
scipy	11
pandas	13
hpc	24
gpus	6
essential	4
efficient	8
neural	5
network	5
training	14
parallel	29
hyperparameter	3
optimization	4
under	2
uncertainty	2
workflow	16
leverage	3
batch	10
scheduling	4
system	11
enable	4
reproducible	4
high-throughput	6
across	5
peak	3
utilizes	3
python-based	6
environment	7
managed	3
miniconda	4
key	6
include	20
developing	4
generative	2
flow	9
3d	5
process	9
involves	9
medical	4
image	13
preprocessing	5
segmentation	6
research	11
primarily	14
computing	16
ecosystem	4
core	6
additional	5
matplotlib	8
metagenomic	3
structure	9
sequences	3
current	3
sequence	10
several	4
domain	4
analyses	15
filtering	4
clustering	3
primary	5
computational	14
task	2
protein	2
set	4
estimate	3
10	4
full	3
dataset	5
however	2
efficiency	2
plan	4
nvidia	3
stages	3
allows	2
resources	11
while	3
times	3
each	2
stage	2
weeks	2
storage	7
requirements	5
15	2
tb	2
files	10
within	8
efficiently	3
scikit-learn	9
associated	6
utilise	3
developed	14
pipelines	14
bioinformatic	3
analysis	56
genome	8
sequencing	13
packages	25
usage	2
samtools	28
minimap2	4
custom	12
scripting	4
bash	8
r	84
compute	10
	53
stack	6
science	3
inference	3
imaging	4
toolkits	4
monai	2
open	13
ai	3
loss	2
functions	4
2d	2
algorithms	6
implementation	3
object	3
detection	4
cellpose	2
cell	6
architectures	5
opencv	6
scikit-image	4
normalization	2
reduction	3
classical	3
methods	11
divided	2
three	2
computationally	5
intensive	5
high-resolution	2
images	3
geometric	2
improve	2
model	17
gpu	15
accelerated	2
segment	2
requires	10
acceleration	2
cuda	10
handle	5
iterative	3
large	23
datasets	19
perform	8
automated	2
conduct	2
comparative	2
performance	7
most	5
requirements	2
parallelization	2
slurm	10
multiple	9
patient	2
sets	2
memory	10
high-memory	4
nodes	11
required	14
stacks	3
during	3
access	15
phases	2
cpus	2
mhd	3
code	21
github	12
io	10
written	12
fortran	15
parallelised	7
mpi	13
openmp	8
pseudo-spectral	4
uses	16
radial	2
spherical	3
harmonics	2
shell	5
post-processing	4
development	3
networks	4
time-series	3
text	5
monte	2
carlo	2
techniques	5
quantification	6
levels	3
extensive	3
experiments	4
embedding	2
sizes	4
fusion	2
strategies	4
tasks	8
studies	2
calibration	2
computation	5
evaluate	3
anything	2
transformers	4
generated	2
includes	3
machine	10
workflows	11
involve	5
scale	3
fine-tuning	2
multi-modal	3
feature	3
extraction	5
high-performance	4
vram	2
fast	3
capacity	2
intermediate	4
outputs	8
transcriptomics	5
proteomic	2
bulk	4
single	2
cellranger	7
fastqc	17
fastq	3
comet	7
beta	3
anaconda	11
java	8
relies	2
both	6
because	2
distributed	3
cluster	6
still	2
necessary	4
nextflow	2
containerised	3
cutadapt	3
amplicon	3
multiqc	9
modules	13
modular	4
blast	8
ansys	21
workbench	7
very	3
fine	2
mesh	4
facility	7
rna-seq	5
single-cell	2
scrna-seq	4
pipeline	13
bioinformatics	19
quality	12
control	11
trimmomatic	3
adapter	2
trimming	3
star	17
hisat2	6
read	10
alignment	12
reference	2
genomes	2
transcript	2
featurecounts	3
salmon	10
kallisto	2
followed	2
downstream	11
statistical	18
bioconductor	2
deseq2	3
ranger	3
seurat	5
scanpy	4
annotation	7
addition	2
following	5
julia	11
matlab	61
capabilities	4
rna	6
long-read	4
ont	2
structural	5
variants	3
conducted	4
appropriate	2
bamtools	7
bedtools	15
study	3
regions	2
file	7
ondemand	6
signac	2
scenic	2
tidyverse	7
utilises	2
designed	2
gpu-l	3
framework	4
utilising	2
docker	3
ensure	7
reproducibility	2
configured	2
operations	2
directly	2
engineering	4
sensor	2
graphs	2
geopandas	3
complex	5
specifically	3
graph	2
"	2
allow	3
it	10
intended	5
et	2
al	2
solves	2
transport	2
gaussian	13
chemistry	2
where	5
expect	2
few	2
minutes	2
hours	3
time	8
implemented	4
spatial	7
visualization	4
typical	3
handling	10
netcdf	6
existing	2
products	2
memory-intensive	3
dna	5
dorado	2
open-source	4
assembly	5
verkko	2
routinely	2
snps	2
established	3
languages	2
analyse	3
visualisation	12
differential	3
gene	3
expression	3
widely	2
adopted	2
functional	8
enrichment	2
databases	2
executed	8
interactive	3
multi-core	3
cpu	9
moderate	2
workloads	6
execution	2
resource	2
scripts	16
future	2
samples	2
qc	7
merging	2
trim	3
galore!	2
samtools	2
picard	9
design	3
test	3
sample	4
largely	2
cover	2
mechanical	2
fea	2
only	2
lammps	9
bcftools	15
built	4
biocmanager	3
provide	2
functionality	4
genomic	2
processed	2
change	2
over	5
analytical	2
xshells	2
c	25
spectral	2
method	3
solve	2
magnetohydrodynamics	2
equations	3
rotating	2
geometry	4
fourier	2
library	7
fftw	7
employed	3
parallelisation	2
done	3
mode	2
hybrid	4
fluid	5
source	9
mapping	6
calling	8
openfoam	9
code_saturne	2
senga-ops	2
in-house	8
infrastructure	2
then	2
script	2
final	4
amount	3
tests	7
well	8
take	3
days	2
intend	2
jupyter	7
part	8
form	2
make	5
common	2
jax	5
optimisation	3
arrays	3
environments	4
singularity	3
ml	2
solver	5
spins	2
navier-stokes	2
case	4
four	2
you	2
must	2
suite	7
phylogenetic	2
eggnog-mapper	2
making	4
bigstatsr	2
bigsnpr	2
integrated	2
genetics	4
plink	7
rapid	2
through	4
genotype	2
generation	4
shared	2
statically	2
compiled	3
binaries	2
two	2
linux	10
bam	2
handing	2
viewing	2
interrogation	2
aligned	2
benchmarks	2
vcf	2
normalisation	2
variant	9
calls	5
gatk	13
mutect2	2
indel	3
mutserve	2
mitochondrial	2
caller	3
snv	2
haplocheck	2
contamination	2
checker	2
aligners	2
bwa	15
bowtie	4
spades	5
megahit	3
along	5
microscopy	2
main	3
added	2
programme	2
torch	3
torchvision	2
team	4
runs	5
mainly	7
produce	4
frames	2
chains	2
plots	4
relevant	2
quantum	8
state	3
art	2
fft	3
rk4	2
sampling	2
mcmc	3
*	2
force	2
field	2
toolkit	3
bespoke	4
openmm	2
gromacs	4
molecular	7
dynamics	3
free	3
potentials	3
simulation	7
signal	2
quantitative	2
accuracy	3
robustness	2
interaction	2
liana	2
basic	7
rstudio	6
sas	2
dft	2
molecules	2
espresso	5
calculations	3
vasp	5
integrates	2
orca	5
yolo	3
classification	2
git	5
user	2
space	2
transient	3
students	3
fsl	5
their	3
enables	2
applications	2
vep	6
reads	3
call	3
input	2
interpretation	2
output	4
group	2
sniffles	2
callers	2
alongside	2
investigate	3
high	6
high-dimensional	2
workload	3
significant	2
more	5
stan	3
notebook	4
visualise	4
results	3
approximately	3
cores	2
ram	4
complete	3
generate	6
production	2
conjunction	2
video	2
initial	4
found	2
higher	2
about	2
long	5
node	3
takes	2
right	2
maximum	2
order	4
electronic	4
states	2
www	14
unix	3
manager	3
small	2
programming	5
finite	3
difference	2
reacting	2
amr	2
high-speed	2
flows	2
cfd	6
problems	2
industry	2
wide	2
variety	2
command-line	4
acceptable	2
members	3
utilities	5
working	4
solvers	3
rocket	5
dynamics	6
center	2
sciences	2
lawrence	2
berkeley	2
national	2
laboratory	2
further	3
details	3
amrex-combustion	2
pelelmex	2
screening	2
clusters	2
gfortran	4
potentially	2
paraview	4
compiler	6
package	8
tested	2
fluent	9
dedalus	2
request	2
us	2
after	2
combined	2
programs	2
combination	2
generic	3
sandia	2
ngs	2
wes	3
bio	2
projects	2
stata	5
keras	4
intel	5
studio	11
cmake	2
gnu	2
compile	2
employ	2
	2
decomposition	2
parallelism	2
emacs	2
statistics	3
jdk	2
release	2
gcc	6
preferably	2
aligner	3
perl	8
out	2
various	2
compiling	2
dependencies	2
targeted	2
fastp	4
human	3
hostile	2
bowtie2	7
bacterial	3
taxonomic	2
profiling	3
metaphlan	2
humann	2
biobakery	2
bwa-mem	3
checkm	2
metabat2	2
dada2	3
kraken2	3
mothur	3
s-andrews	2
en	4
linux_x64_install	2
html	5
broadinstitute	3
tag	2
arq5x	2
bedtools2	2
htseq	3
readthedocs	2
cran	2
r-project	2
bin	2
ubuntu	4
fullreadme	2
hc	2
en-us	2
articles	3
360036194592-getting-started-with-gatk4	2
downloads	2
align	2
rnaseq	4
technology	2
types	2
skills	2
impact	2
computer	3
do	3
nanopore	2
being	3
selection	3
conda	5
tophat	3
analysing	2
integration	3
multi-omic	2
interactions	2
genomics	8
comsol	3
simulator	2
pip	2
population	4
due	2
go	2
hdf5	4
gdal	2
python3	2
snptest	2
number	2
agisoft	2
macs2	2
spaceranger	3
pre-processing	2
density	2
theory	2
machine-learning	2
systems	5
automation	2
together	3
aimpro	2
gnuplot	2
jmol	2
phd	2
nbo	2
useful	2
hugging	2
face	2
tumours	2
mpi-based	2
shared-memory	2
nucleotide	2
simple	2
mtdna	2
tool	2
doi	2
trinity	2
deeplabcut	2
features	2
afni	2
freesurfer	2
producing	2
alignments	2
provides	2
range	2
genetic	2
many	2
high-quality	2
multiphysics	2
stable	2
fmrib	3
docs	3
ab	2
initio	2
nmr	3
visual	2
cfx	2
multiphase	3
coupled	2
ggplot2	2
mkl	2
toolboxes	2
scikit	2
dsi-studio	2
labsolver	2
modules	2
surfer	2
mgh	2
harvard	2
fslwiki	2
vcftools	5
10x	2
muon	2
epitrace	2
pseudotime	2
epi2me	2
nf-core	2
scnanoseq	2
recent	2
admixture	3
phylogenomics	3
iqtree	3
beast	4
supports	2
ncbi	2
nih	2