BOL: Related items

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

Rahul Nayak — Tue, 03 Jul 2018 05:05:55 -0500

NAViGaTOR – Network Analysis, Visualization, & Graphing TORonto is a software system for scaleable visualizing and analyzing networks. The current version, NAViGaTOR 3, increases modularity, improves scaleability, extends input/output options, brings new network views and analysis algorithms. http://142.150.188.236/navigatorwp/

Address of the bookmark: http://142.150.188.236/navigatorwp/

JASMINE: Jointly Accurate Sv Merging with Intersample Network Edges

Shruti Paniwala — Sat, 02 Jul 2022 11:41:53 -0500

This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples.

Address of the bookmark: https://github.com/mkirsche/Jasmine

Patterns: a modeling tool dedicated to biological network modeling

Abhimanyu Singh — Fri, 26 Jul 2019 01:11:59 -0500

It is designed to work with patterned data. Famous examples of problems related to patterned data are:

recovering signals in networks after a stimulation (cascade network reverse engineering),
analysing periodic signals.

Address of the bookmark: https://github.com/fbertran/Patterns

Useful links to therapy, disease, drug and drug-target network data:

Jit — Mon, 01 Jun 2020 11:47:51 -0500

Useful links to therapy, disease, drug and drug-target network data:

DrugBank:

a bioinformatics- cheminformatics resource combining detailed drug data with comprehensive drug target information with >4900 drug (~3500 experimental) and >1500 non-redundant protein entries http://www.drugbank.ca/

Drug-Target Network:

network data of 890 drugs and 394 target human proteins http://www.nature.com/nbt/journal/v25/ n10/suppinfo/nbt1338_S1.html

Drug-Therapy Network:

three layers of drug-therapy networks according to the ATC classification http://www.biomedcentral.com/1471-2210/8/5/additional/

FDA Orange Book:

approved drug products with therapeutic equivalence evaluations http://www.fda.gov/cder/ob/HIDdb: Thomson Investigational drugs database including information on 107000 patents, 25000 investigational drugs and 80000 chemical structures http://scientific.thomson.com/products/iddb/HOMIM: a knowledgebase of human genes and genetic disorders http://www.ncbi.nlm.nih.gov/ sites/entrez?db=omim

PDTD:

3D drug target structure database with a target identification option http://www.dddc.ac.cn/pdtd/

Predicted drug targets:

a set of 1383 predicted drug targets http://www.biomedcentral.com/1471-2105/8/353/additional/ [25] Protein ligand network: a network of 4208 ligands and ~15000 binding sites http://pbil.kaist.ac.kr/~parkkw/Lnet/

TDR Targets Database:

identification and ranking targets against neglected tropical diseases http://tdrtargets.org/

Therapeutic Target Database:

lists >1500 therapeutic targets, disease conditions and corresponding drugs http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp