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Open Screening Environment is a open source system for management of High Throughput Screening related experiments. The platform consists of new research tools that will enhance significantly management and analysis of HTS data. More information can be f
RENCO is a C++ based software for automatic generation of ordinary differential equations for gene and protein expression dynamics in artificial regulatory networks.
A Folding@Home integrated monitoring environment, designed for Linux, *nix systems and Windows, which is intended to be easy-to-use and provide a flexible, customiseable and "user-friendly" environment for reviewing the status of active F@H clients.
ChemCpp is a C++ toolbox for chemoinformatics focusing on the computation of kernel functions between chemical compounds. Together with Support Vector Machines, these kernel functions find natural applications for virtual screening of molecules.
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SISSIz is a program for randomizing multiple sequence alignments preserving dinucleotide content. It can be used as a control strategy for comparative noncoding RNA gene prediction programs and as a standalone RNA gene finder.
XAS is a software with graphical user interface to performan analysis of data generated by a high-throughput expression cloning technology using gene expression microarrays.
Parallel IBDWS is an upgrade from IBDWS that utilizes parallel processing. Also, the incorporation of DNA sequence data has been added since the last code release
This is a mathematical/informatical/biologocal aproach to System-research. The aim is to write a progrramm that simulates a world with as many mathematical methods as possible at once.
Here is a repository of libraries automatically generated by Patlac::Xml2cpp software.
All of these libraries are c++ translation of their respective xsd schema. They include classes with accessors, saxparser with iteration mode and xml serialization.
IGBM (Identification of gene blocks in microorganisms) implements a BLAST-like method to infer conserved gene clusters among closely related prokaryotes, and provides a graphical user interface to navigate the identified clusters and their annotated info
The BioArray Software Environment (BASE) v1.2 is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis. PrognoChip-BASE extends BASE v1.2.16, providing more functionalities.
Mito-MAS-m is a simulator of the mitochondrial inner membrane and the enzymatic complexes embedded in it, implementing a coarse-grained (CG) model of the molecules using rigid structures and Dissipative Particules Dynamics (DPD) as motion equation.
SpiNet is a neural simulation tool for large spiking networks with highly heterogeneous synapses. Neurons are modelled as I&F units with dual exponential synaptic conductances. Complex network models can be easily built using the included tool NetBuilder
NOTE: The IntAct package is now hosted at google code: http://intact.googlecode.com IntAct is an open source package to store and manipulate molecular interaction data.
We present a maximum-likelihood method for examining the selection pressure and detecting positive selection in noncoding regions using multiple aligned DNA sequences.
Neurofitter is a parameter tuning package for electrophysiological neuron models. For more information please take a look at http://neurofitter.sourceforge.net
GeneIndex is a parallel program using MPI. It finds frequencies and positions of all words of a certain length in a DNA sequence. Large genome will be an ideal target of GeneIndex.
Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees.