Efficient solutions for mapping parallel programs

Drug discovery as well as (nano)material design projects demand the in silico analysis of large datasets of compounds with their corresponding properties/activities, as well as the retrieval and virtual screening of more structures in an effort to identify new potent hits. This is a demanding procedure for which various tools must be combined with different input and output formats. To automate the data analysis required we have developed the necessary tools to facilitate a variety of important tasks to construct workflows that will simplify the handling, processing and modeling of cheminformatics data and will provide time and cost efficient solutions, reproducible and easier to maintain. We therefore develop and present a toolbox of >25 processing modules, Enalos+ nodes, that provide very useful operations within KNIME platform for users interested in the nanoinformatics and cheminformatics analysis of chemical and biological data. With a user-friendly interface, Enalos+ Nodes provide a broad range of important functionalities including data mining and retrieval from large available databases and tools for robust and predictive model development and validation. Enalos+ Nodes are available through KNIME as add-ins and offer valuable tools for extracting useful information and analyzing experimental and virtual screening results in a chem- or nano- informatics framework. On top of that, in an effort to: (i) allow big data analysis through Enalos+ KNIME nodes, (ii) accelerate time demanding computations performed within Enalos+ KNIME nodes and (iii) propose new time and cost efficient nodes integrated within Enalos+ toolbox we have investigated and verified the advantage of GPU calculations within the Enalos+ nodes. Demonstration data sets, tutorial and educational videos allow the user to easily apprehend the functions of the nodes that can be applied for in silico analysis of data.

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Parallel Computing Using the Prefix Problem

10.1093/oso/9780195088496.001.0001 ◽

1994 ◽

Author(s):

S. Lakshmivarahan ◽

Sudarshan K. Dhall

Keyword(s):

Parallel Computing ◽

Parallel Algorithms ◽

Parallel Programming ◽

Building Blocks ◽

Efficient Solutions ◽

Computer Scientists ◽

Important Approach

The prefix operation on a set of data is one of the simplest and most useful building blocks in parallel algorithms. This introduction to those aspects of parallel programming and parallel algorithms that relate to the prefix problem emphasizes its use in a broad range of familiar and important problems. The book illustrates how the prefix operation approach to parallel computing leads to fast and efficient solutions to many different kinds of problems. Students, teachers, programmers, and computer scientists will want to read this clear exposition of an important approach.

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