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The Workbench for Integrative Systems Biology is a portal-based workbench for interdisciplinary systems biology projects

 

Web-based tool for the visualization and interrogation of Campylobacter jejuni glycomics pathway

 

Progol code and interpreter to perform Inductive Logic Programming using a Prolog knowledge base

 

PINALOG is a novel approach to align two protein-protein interaction (PPI) networks which combines information available for the proteins in the networks, including sequence, function and network topology

 

This tool performs automated translation of models of biochemical systems written in a natural language-like syntax into a program in Microsoft Research's stochastic simulation language (SPiM) for π calculus

 

Online tool for analysis of public microarray data sets, enabling selection of gene sets that exhibit differential expression under specified conditions

 

ABC-SysBio is a tool for parameter inference and model selection used in the analysis of Hes1 qRT-PCR data from sub-project 3

 

XperimentR is a user friendly web enabled software tool that has been designed to ease the pain of annotating biological experiments and laboratory processes

 

The XperimentR Ontology Service is a minimal software application developed to support the Terminize and Minimal Information Template features of XperimentR. It provides a JSON/HTTP API to search for terms in some or all of the ontologies or controlled vocabularies that have been loaded into the database

 

Lightweight data management system for Waters UPLC/ESI-MS/MS, Waters MALDI-TOF-MS and Bruker NMR data

 

Radar is a simple web-based inventory of the outputs from research projects, such as articles, datasets and software

 

ADAM is a storage system for research data that performs automated indexing to provide powerful search, discovery and collaboration features without the requiring the use of a structured repository

 

OMERO is a software application for storage, visualisation and analysis of biological microscope images. We have developed extensions to OMERO to support Active Directory and Definiens integration. These are available on request.

Prolog clauses representing background knowledge relating to Campylobacter capsule formation

 

A comparison of the transcript profiles of mutants in capsule locus genes from Campylobacter jejuni strain 13362 compared to wild type

 

Treatment of Campylobacter jejuni wild type strain NCTC 13362 with various infection or environmental mimic perturbations

Transcriptional profiles of capsule locus mutants compared to wild type Campylobacter jejuni strain NCTC 13362. RNA was extracted after incubation optimized to give maximal capsule expression in the wild type cells

 

Metabolomic characterisations of Campylobacter jejuni mutants as determined by 1H NMR

 

Zeiss LSM imaging of bacterial phagocytosis

 

Zeiss LSM imaging of bacterial phagocytosis

 

AVI visualisation of 3D simulation of phagocytic engulfment

 

Murine dendritic cells were differentiated from the bone marrow of 15 C57Bl/6 mice (8-12 weeks old) for 8 days in the presence of GM-CSF. On day 8, cells were harvested, pooled and 1.5x106 cells were seeded into 6-well plates pre-coated with the Notch ligand Jagged-1 (Fc fusion protein) or IgG1 (control) in the presence or absence of the TLR4 ligand LPS (100ng/ml). Cells from 3 wells per condition were harvested every 30 mins for 4 hrs.

 

Murine dendritic cells were differentiated from the bone marrow of 20 C57Bl/6 mice (8-12 weeks old) for 8 days in the presence of GM-CSF. On day 8, cells were harvested, pooled and 1.5x106 cells were seeded into 6-well plates pre-coated with the Notch ligand Delta-like 1 or Jagged-1 (both were Fc fusion proteins) or IgG1 (control) in the presence or absence of the TLR4 ligand LPS (100ng/ml). Cells from 3 wells per condition were harvested at 0h, 1h, 2h and 4h.

 

Dendritic cells were differentiated from bone marrow. Rat Jgd1/humanFc fusion protein (R&D Systems) or human IgG1 (Sigma Aldrich) (control samples) were immobilized onto tissue culture plates (10 μg ml−1 in PBS) overnight at 4 °C. Dendritic cells were spun onto the plate and cells were collected at the appropriate time. Total RNA was isolated using the Absolutely RNA micro prep kit (Stratagene). Complementary DNA was generated from 125 ng of total RNA using an archive kit (Applied Biosystems). 1 μl of cDNA was used with PCR Mastermix and TaqMan primer and probes (both Applied Biosystems) and analysed on an Applied Biosystems 7500 PCR system. Cycle thresholds were normalized to 18S and calibrated to a PBS-treated control sample for relative quantification.

 

Analysis of the impact of M. bovis on 1H NMR metabonomic profiles of urine samples from infected cows

MATLAB code for the analysis of microscopy images of bacterial phagocytosis

 

Surface Evolver code for the simulation of bacterial phagocytosis

 

Compositional process algebra models of actin polymerisation and a geometric representation of these models that allows movies to be generated reflecting their dynamics

 

PIM model and corresponding SPiM representation of Fcγ receptor phosphorylation during phagocytosis (from http://dx.doi.org/10.4204/EPTCS.9.9)

 

Description of the mathematical model developed to simulate the progression of tuberculosis infection in a single host