RMOD identifies regulatory motifs and their properties in signaling networks. paper

COFECO annotates protein complexes & cellular functions of input genes & their orthologs. paper

DynaMod identifies dynamic functional modules from the gene expression profiles in different conditions. paper

CLIC an individual dimension based clustering method for large microarray datasets optimized cluster number. paper

BICLIC searches comprehensive sets of biclusters in gene expression datasets. paper

FIGS selects significant genes from gene expression profiles comparing different statistics & classifiers. paper

IDDI predicts domain-domain interactions database and web-interface. paper

HMPAS a comprehensive collection & analysis system for human membrane proteins. paper

SKNN imputes missing data using modified K-nearest neighbor algorithm with reuse of imputed data. paper

PKMiner searches candidates of type II PKS gene clusters and their polyketide chemotypes in actionbacterial genomes. paper

PTMFinder an advanced PTM identification method from tandem mass spectroscopy. (32bit Only) paper

ComBiCom an integrated public protein-protein interaction and protein complex database. paper

PTM-SNP a collection of SNPs influencing PTMs with their disease information. paper

ScaffoldNet a collected known scaffold protein and predicted scaffold protein candidates databases.

 

 

Computing Servers

Synbimics (60 nodes) CPU  Total main memory: 2.82 TB HDD 32 TB Total 42.15 TFLOPS in single precision Intel Xeon Processor X5650 (7EA) Intel Xeon Processor E5-2630 (7EA) Intel Xeon Processor E5-2630 v2 (10EA) Intel Xeon Processor E5-2630 v3 (25EA) Intel Xeon Processor E5-2640 v4 (5EA) Intel Xeon Processor Gold 6230R (10EA)   GPU (AI Learning Server) Total 89.48 TFLOPS in single precision NVIDIA Tesla K80 (2*2496 cores, 2*240GB/s, 24GB) 2EA, PCIE 3.0 x16 NVIDIA Tesla P40 (3840 cores, 346GB/s, 24GB) 6EA, PCIE 3.0 x16	Biomics (9 nodes)   CPU  Total main memory: 216 GB HDD 1.3TB Total 1.35 TFLOPS in single precision Intel Xeon Processor E5530 (9EA)	Structure Modeling Server CPU Total main memory: 256GB HDD 4.5TB Total 1.73 TFLOPS in single precision Intel Xeon Processor E5-2670 v3 (2EA)   GPU Total 7.11 TFLOPS in single precision NVIDIA Quadro K5200 (2304 Cores, 192GB/s, 8GB) PCIE 3.0 x16	SynbiDrug GPU server (24 nodes) LEADERS-SV8000-GSx8 X 3 Total 376.8 TFLOPS in single precision System Interface NVIDIA NVlink Mellanox InfiniBand 100GB/s HDD 12TB 3EA SSD 4TB 3EA Tesla V100 SXM2 (5120 cores, 900GB/s, 32GB) 24EA  12x HHHL(x16) PCIe Card

 

 

Molecular & Cellular Analysis Systems

High Contents Screening Imaging System (Molecular Device)	Confocal Image Microscopy (Nikon)	Real-Time PCR Detection System (BioRad) Two-target analysis	Luminex 200 System with xPONENT 3.1 (Luminex Corporation) Laser-based fluorescence Classification laser, Reporter laser, Reporter detector  100 different analytes per sample	Multi-label Reader Victor X4 (PerkinElmer) Fluorescence, Absorbance, Luminescence, Time-resolved fluorometry, filter: 340-850nm

 

 

Frequently Used External Resources

1. Genomic Sequence Analysis

RefSeq a set of reference sequences including genomic, transcript, and protein. paper

Entrez Gene a portal to gene-specific content based on NCBI's RefSeq project. paper

UniGene a resource of transcripts from the same locus, expression, health status, and related proteins. paper

WTCCC provides genotype data for up to 500,000 sites of genome sequence variation. paper

GWAS Catalog a catalog of published genome-wide association studies. paper

dbSNP provides single base nucleotide subsitutions and short deletion/insertion polymorphisms. paper

PLINK an open-source whole genome association analysis toolset. paper

UCSC Genome Browser contains the reference sequence and working draft assemblies for a collection of genomes. paper

Ensembl tools and data resources to facilitate genomic analysis in chordate species. paper

ClustalW2 DNA or protein multiple sequence alignment program. paper

Ensembl compara provides cross-species resources and analyses, at both the sequence level and the gene level. paper

HAPMAP provides genetic similarities and differences in human beings. paper

 

2. Gene Expression Analysis

Gene Expression Omnibus a database for high-throughput gene expression data. paper

Array Express a database of functional genomics experiments from microarray and high throughput sequencing studies. paper

CGAP a database of gene expression profiles of normal, precancer, and cancer cells. paper

Allen Brain Atlas a database of gene expression patterns in the mouse brain. paper

Connectivity Map  a database of gene-expression profiles from cultured human cells treated with bioactive small molecules. paper

TRANSFAC a database of eukaryotic transcriptional regulation, TFs, target genes and regulatory binding sites. paper

TcoF a database of human transcription factors and the transcription cofactors with which they interact. paper

Tfcat a database of mouse and human TFs based on annotations obtained by expert review of the scientific literature. paper

MINDy a tool to discover modulator inference by network dynamics. paper

ARACNE a tool to elucidate gene regulatory network using microarray expression profiles. paper

MATCH a tool for searching transcription factor binding sites in DNA sequences. paper

 

3. Function & Disease Analysis

Gene Ontology a database of representation of gene and gene product attributes across all species. paper

Panther Ontology uses the Gene Ontology but was adapted from the PANTHER/X molecular function ontology. paper
KEGG Brite a collection of functional hierarchies of various biological objects. paper

DAVID a comprehensive set of functional annotation tools to find biological meaning behind large list of genes. paper

OMIM a comprehensive, authoritative compendium of human genes and genetic phenotypes. paper

PharmGKB Disease a pharmacogenomics knowledge resource, partly disease. paper

Genetic Association DB a database of genetic association data from complex diseases and disorders. paper

Cancer Gene Census a list of genes for which mutations have been causally implicated in cancer. paper

HGMD a database of human gene mutation data. paper

InnateDB a publicly available database related to innate immune response. paper

PDBTM transmembrane protein selection of the Protein Data Bank. paper

dbGaP a database of genotypes and phenotypes. paper

TCDB provides functional and phylogenetic classification of membrane transport proteins. paper

TOPDB a collection of transmembrane protein datasets containing experimentally derived topology information. paper

gpDB contains G-proteins and their interactions with GPCRs and effector molecules. paper

Organelle DB compiles protein localization data of organelles, subcellular structures, and protein complexes. paper

DBSubLoc a database of protein subcellular localization. paper

LOCATE a curated database of the membrane organization and subcellular localization of proteins. paper

eSLDB a database of protein subcellular localization annotation for eukaryotic organisms. paper

 

4. Protein Analysis & Engineering

Uniprot a database of protein sequence and functional information. paper

BioGRID a biological general repository for interaction datasets. paper

DIP a database of interacting proteins. paper

IntAct a molecular interaction database. paper

MINT a molecular interaction database. paper

MIPS MPPI a mammalian protein-protein interaction database. paper

MPIDB provides all known physical microbial interactions. paper

MIPS CORUM provides a resource of manually annotated protein complexes from mammalian organisms. paper

InterPro classifies proteins into families and predict domains and important sites. paper

Pfam a large collection of protein families, each represented by MSA and HMM. paper

Prosite consists of protein domains, families and functional sites as well as associated patterns and profiles. paper
Gene3D a database of CATH v4.0 protein domain assignments for ENSEMBL and UniProt sequences. paper

3did a collection of high-resolution three-dimensional structural templates for domain-domain interactions. paper

iPfam a catalog of protein family interactions, including domain and ligand interactions, calculated from known structures. paper

DOMINE a database of known and predicted protein domain (domain-domain) interactions. paper

PDB an information portal to biological macromolecular structures. paper

DBPTM an informative resource for protein post-translational modifications (PTMs). paper

UbiProt a resource of ubiquitination experimentally obtained. paper

SCUD provides the information about ubiquitinated proteins as well as related enzymes in S. cerevisiae. paper

UNIMOD a resource of protein modifications for mass spectrometry. paper

HistoneCode a tool for analyzing correlation of histone modification. paper

 

5. Network Analysis & Engineering

KEGG pathway a collection of manually drawn pathway maps. paper

NCI-PID a free biomedical database of human cellular signaling pathways. paper

BioCarta an interactive graphic models of molecular and cellular pathways. paper

Panther Pathway consists of pathways with subfamilies and protein sequences mapped to individual pathway components. paper

Reactome a curated and peer reviewed pathway database. paper

Wikipathway an open, public platform dedicated to the curation of biological pathways. paper

PathwayCommons a biological pathway resource collected from public pathway databases. paper

Pathway studio a tool to analyze and visualize cellular mechanisms derived from published scientific data. paper

Cytoscape a network visualization tool. paper

KEGG viewer a KEGG pathway figure editing tool. paper

 

6. Modeling & Simulation

UciNet a software package for the analysis of social network data. paper

FANMOD a tool for fast network motif detection. paper

Biomodels Database a repository of computational models of biological processes. paper

The Cell Collective consortium for logical models and tools. paper

CellNOpt creates logic-based models of signal transduction networks using different logic formalisms. paper

Boolesim boolean simulator with user defined network. paper

Pantograph a software toolbox to reconstruct, curate and validate genome-scale metabolic models. paper

CellDesigner a process diagram editor for gene-regulatory and biochemical networks  paper

GINsim a computer tool for the modeling and simulation of genetic regulatory networks paper

BoolNet  an R package for generation, reconstruction and analysis of Boolean networks paper

NetDS a Cytoscape plugin to analyze the robustness of dynamics and feedforward/feedback loop structures of biological networks paper

BooleanNet intuitive and accessible tools for simulating biological regulatory networks in a boolean formalism paper

Bio Model Analyzer (BMA) a visual Tool for Modeling and Analysis of Biological Networks paper

Bio-SPICE a biological Simulation Program for Intra- and Inter-Cellular Evaluation paper

The Virtual Cell (Vcell) a unique computational environment for modeling and simulation of cell biology paper

e-cell a software environment for whole-cell simulation paper

IPA a tool to model, analyze, and understand the complex biological and chemical systems. paper

FMM reconstructs metabolic pathways form one metabolite to the other one. paper

CoLoMoTo reconstructs metabolic pathways form one metabolite to the other one. paper

 

7. Drug Analysis & Engineering

PharmGKB Drug a pharmacogenomics knowledge resource, partly drug. paper

IUPHAR-DB an expert-driven guide to pharmacological targets and the substances that act on them. paper

Binding DB a database of binding affinities, focusing on the interactions of protein considered to be drug-targets. paper

STITCH provides protein–chemical interactions with experimental & manually curated evidence with text-mining/predictions. paper
SIDER a database of side effects of drugs. paper

PDSP Ki provides drug interaction with molecular targets, affinity and drug candidates. paper

TCM database a database of Traditional Chinese Medicine. paper

TCMID Traditional Chinese Medicine integrative database for herb molecular mechanism analysis. paper

NPBANK a website of about 300 chemical components of Natural Products. paper

CAS Database provides accurate and authoritative chemistry content paper

Scifinder is a research discovery application that provides substances and reactions in chemistry and related sciences paper

DoBISCUIT a secondary metabolite database. paper

2metDB a secondary metabolite database. paper

ClusterMine360 a database of microbial PKS/NRPS biosynthesis. paper

PKSDB a database of Modular Polyketide Synthases. paper

MapsiDB an integrated web database for type I polyketide synthases. paper

 

8.  Bio Tools

In cell protein interaction assay - FRET (Fluorescence Resonance Energy Transfer), BiFC (Biomolecular Fluorescence Complementation),  BRET(Bioluminescence Resonance Energy Transfer)

Diabetes cell assay -  Glucose Uptake, Oil red O staining, Triglyceride assay

Cancer cell assay - Cell proliferation & viability(MTT assay, EdU incorporation), Apoptosis(PI/Annexin V staining), Cell cycle(Mitotic index, Nuclear staining) analysis

Post-Translational Modification analysis - Ubiquitination (in vitro, in vivo ubiquitination assay, Degradation assay), Phosphorylation(Phospho-antibody based western blot)

ClinicalTrials.gov   a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world paper

 

9. BT Supporting Tools

Biology WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. paper

NEB Interactive Tools an experimental design tools for restriction enzymes. paper

GenScript Bioinformatic Tools an experimental design tools for primer design, siRNA, etc. paper

Primer3 a tool to design and analyze primers for PCR and real time PCR experiments. paper

The Sequence Manipulation Suite a collection of web-based programs for analyzing and formatting DNA and protein seq. paper

fr33.net contains sequential converter, translater, alignment, etc. paper

Science Gateway Tools a community-developed set of tools that are integrated through a portal or a suite of applications. paper

Chromas  opens chromatogram files. paper

ImageJ an image processing and analysis tool. paper

FDA_IND  Investigational New Drug (IND) Application paper

Genevestigator  comprehensive fully curated and globally normalized resource of gene expression for biopharmaceutical and medical research