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http://www.pensoft.net/index.php

Publisher that specializes in academic and professional book and journal publishing, mostly in the field of biodiversity science and natural history. They are academic publishers based in Eastern Europe with more than 600 books and e-books published so far. They largely perform their activities in English, with only a minor fraction of publications being in French, German, Russian and Bulgarian. Pensoft is also involved as a publisher in several European Union Fp5, FP6 and FP7 projects where they have specialized in dissemination, communication and publishing; as well as in creating and maintaining websites and Internal Communication Platforms (ICP), designing of logos, flyers, leaflets and posters. Open-access journals include ZooKeys, BioRisk, and PhytoKeys. ZooKeys is a journal in biodiversity science and has implemented several innovations in digital publishing and dissemination including developing and implementing an XML-based submission, editorial, publication and dissemination workflow. The TRIADA platform, for publishing, disseminating and marketing of printed books, e-books and open access journals, provides a linked environment for content, authors, reviewers, editors and customers through four independent classifications (taxonomic, subject, geographical, and geological time scale) as well through tagging and semantic mark-up. TRIADA uses a one-time registration process which allows users to submit, review or edit manuscripts, to subscribe for E-mail and RSS alerts, and to purchase Pensoft''s products. Web services: Metadata and journal content can be harvested.

Proper citation: Pensoft (RRID:SCR_005903) Copy   

•   Source: SciCrunch Registry

http://www-math.u-strasbg.fr/genpred/spip.php?article3

R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Cascade (RRID:SCR_005861) Copy   

•   Source: SciCrunch Registry

http://www.zmmsoft.com

ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes. ZMM searches optimal structures in the space of generalized coordinates: torsion angles, bond angles, bond lengths, positions free molecules and ions, and orientation of free molecules. Any generalized coordinate may be kept fixed. Molecules and fragments that are not expected to undergo significant conformational changes may be treated as rigid bodies. Popular molecular modeling programs usually work in the space of Cartesian coordinates of atoms. During energy minimization of a big system, many Cartesian coordinates-variables move collectively. For example, rotation of a benzene ring around the C-Ph bond in the Cartesian-coordinates space involves collective motion of 33 variables. In the generalized-coordinates space, this rotation involves variation of just one torsion angle. In ZMM, any fragment of a molecular system may be treated as either rigid or flexible. The generalized-coordinates method saves large computational resources if only a small part of a system is considered flexible. Examples are ligand-protein and protein-protein interactions. The savings occur because the sampling space is reduced and because molecular interactions within rigid fragments are not computed. * ZMM runs on Windows 95, 98, 2000, XP, UNIX, and Linux * ZMM can be used via the command-line interface * ZMM can also be used at Windows via a graphical user interface

Proper citation: ZMM (RRID:SCR_005741) Copy   

•   Source: SciCrunch Registry

http://www.sociopatterns.org/

SocioPatterns is an interdisciplinary research collaboration that adopts data-driven methodology with the aim of uncovering fundamental patterns in social dynamics and coordinated human activity. To achieve its scientific goals, the SocioPatterns collaboration also contributes to the development of new technologies for collecting relevant data. In particular, the collaboration supports the development of the SocioPatterns sensing platform, which uses wireless wearable sensors to gather longitudinal data on human mobility and face-to-face proximity in real-world environments. The SocioPatterns team also works on developing tools and techniques to represent, analyze and visualize the collected data. We increasingly use digital media and computational devices in our daily activities, and leave behind a sizable amount of digital traces while doing so. The proliferation of mobile devices, and the incorporation of various sensing technologies in these devices, will further add to this growing trail of data. The possibility to mine and analyze these data, and the scale at which this can be done on contemporary computer systems, affords a novel, data-driven approach in the investigation of various aspects of human behavior. The following collection of datasets obtained through the SocioPatterns sensing platform are available: * Infectious SocioPatterns dynamic contact networks * Hypertext 2009 dynamic contact network * Primary school cumulative networks * Infectious SocioPatterns

Proper citation: SocioPatterns (RRID:SCR_005739) Copy   

•   Source: SciCrunch Registry

http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html

The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape''''s versatile visualization environment to produce an intuitive and customizable visual representation of the results. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: BiNGO: A Biological Networks Gene Ontology tool (RRID:SCR_005736) Copy   

•   Source: SciCrunch Registry

http://www.shuttleworthfoundation.org/

Shuttleworth Foundation is supporting exceptional people to change the world. We provide funding for dynamic leaders who are at the forefront of social change. We identify amazing people, give them a fellowship grant, and multiply the money they put into their projects by a factor of ten or more. We are looking for social innovators who are helping to change the world for the better and are looking for some support through an innovative social investment model.

Proper citation: Shuttleworth Foundation (RRID:SCR_005930) Copy   

•   Source: SciCrunch Registry

http://www.nematodes.org/nematodegenomes/index.php/Main_Page

A collaborative wiki that collates information on completed, ongoing and planned genome and transcriptome sequencing projects on species from phylum Nematoda. The intention is to encourage genome sequencing across the diversity of the phylum Nematoda. Wiki includes: * Published complete nematode genomes: A dynamically generated table of all species for which the genome is published. * Nematode species with genomes in progress: A dynamically generated table of all species for which a genome project is underway. Users may add species to the list * Proposed nematode genome projects: To propose a species for genome sequencing, edit its species page, and set the genome project status to proposed. * BLAST server: Search a number of the nematode-genomes-in-progress with genes of your choice. Currently there are 12 draft genomes available... * Genomes with Data available: Genomes with data available for download. Users may add more data URLs to strain pages or update the URLs.

Proper citation: 959 Nematode Genomes (RRID:SCR_006068) Copy   

•   Source: SciCrunch Registry

http://www.nematodes.org/NeglectedGenomes/MOLLUSCA/index.html

A database housing EST information from nine mollusc species, including Lymnaea stagnalis, the pond snail. Co-curated with Angus davison of Nottingham University.

Proper citation: MolluscDB PartiGene database (RRID:SCR_006069) Copy   

•   Source: SciCrunch Registry

http://mmdb.iab.keio.ac.jp/

MMMDB, Mouse Multiple tissue Metabolome DataBase, is a freely available metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datases are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway. Currently data from cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, and plasma are provided. Non-targeted analyses were performed by capillary electropherograms time-of-flight mass spectrometry (CE-TOFMS) and, therefore, both identified metabolites and unknown (without matched standard) peaks were uploaded to this database. Not only quantified concentration but also processed raw data such as electropherogram, mass spectrometry, and annotation (such as isotope and fragment) are provided.

Proper citation: MMMDB - Mouse Multiple tissue Metabolome DataBase (RRID:SCR_006064) Copy   

•   Source: SciCrunch Registry

http://comgen.pl/mirex/

mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. quantitative real-time PCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. This database aims to be useful to anyone investigating the role of microRNAs in shaping plant development, organ formation and response to different biotic and abiotic stresses. To start exploring the database just press the "Browse Atlas" button or search for a particular microRNA record by typing at least two numbers from its ID in the window.

Proper citation: mirEX (RRID:SCR_006060) Copy   

•   Source: SciCrunch Registry

http://www.fnp.org.pl/en/

The Foundation for Polish Science (FNP), formed in 1991, is an independent, self-financing, non-profit, non-governmental organization, with a mission of supporting science in Poland. It is the largest source of science funding in Poland outside the state budget. The main objectives of FNP are: * to support excellent scientists and research teams, * to facilitate technology transfer, * to support various investment initiatives serving science in Poland. The Foundation realizes these objectives by: * awarding individual prizes and scholarships to scientists, * awarding grants for the modernization of scientific facilities and the protection of scientific collections, * grants for the transfer of scientific achievements to industry, * otherwise supporting important undertakings in the service of science (e.g. through conferences and publishing programs). The Foundation also plays an increasingly active role in supporting international scientific cooperation, taking actions to facilitate the exchange of scientific ideas, and increasing the scientific independence of the younger generation of scientists.

Proper citation: Foundation for Polish Science (RRID:SCR_006062) Copy   

•   Source: SciCrunch Registry

http://afni.nimh.nih.gov/afni/

Set of (mostly) C programs that run on X11+Unix-based platforms (Linux, Mac OS X, Solaris, etc.) for processing, analyzing, and displaying functional MRI (FMRI) data defined over 3D volumes and over 2D cortical surface meshes. AFNI is freely distributed as source code plus some precompiled binaries.

Proper citation: Analysis of Functional NeuroImages (RRID:SCR_005927) Copy   

•   Source: SciCrunch Registry

http://www.biocomputing.it/digit/index.php

The Database of Immunoglobulins and Integrated Tools (DIG IT) is an integrated resource storing sequences of annotated immunoglobulin variable domains of NCBI database and enriched with tools for searching and analyzing them. It contains 145759 heavy chain sequences and 71404 light chain sequences (47168 kappa type and 24236 lambda type) with assigned canonical structures for the hypervariable loops and the data on the type of antigen as well as the pairing information of immunoglobulin heavy and light chains (9672 total pairs). The user can input the immunoglobulin variable domain sequence (amino acid or nucleotide) of interest (heavy chain variable domain sequence; light chain variable domain sequence or both) to retrieve the closest sequences (sorted according to e-value) with complete annotation. The user can also directly query the database by antigen type, canonical structure, germline family in accordance to the requirements.

Proper citation: DIG IT - Database of Immunoglobulins and Integrated Tools (RRID:SCR_005924) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/aLFQ/

An R-package for estimating absolute protein quantities from label-free liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics data. It supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, they used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation.

Proper citation: aLFQ (RRID:SCR_005925) Copy   

•   Source: SciCrunch Registry

http://ftp://lausanne.isb-sib.ch/pub/databases/Bgee/general/IQRray.R

Software based on evolutionary conservation of expression profiles, implemented in R, for identification of poor quality arrays in dataset composed of arrays from many independent experiments.

Proper citation: IQRray (RRID:SCR_006057) Copy   

•   Source: SciCrunch Registry

http://www.neurogems.org/

NeuroGems is a collection of neuroinformatics software modules for data and modelling in neuroscience. The emphasis is on tools for collaboration, visualisation and use of open XML standards. The project was an escience pilot project funded by the UK MRC and BBSRC and based at the Universities of Edinburgh, Newcastle and UCL running from 2002 - 2005. Software Applications available: Textensor, Axiope, NeuroML, neuroConstruct, NClamp, RatBrain, 3D Atlas, Catacomb, Protsim1, Protsim2, Neosim1, Neosim2, Growth, Marching, Voxel, Patterns.

Proper citation: NeuroGEMS informatics software (RRID:SCR_006059) Copy   

•   Source: SciCrunch Registry

http://biodev.cea.fr/interevol/

InterEvol database is designed for the analysis of co-evolution events at the interface of known structures of hetero- and homo-oligomers. The database can be search and analyzed through 3 interconnected levels of analysis: * From a Keyword or the PDB entry of a complex, you can browse: ** structural homologs for every chain in other complexes ** structural interologs for every interface ** retrieve pre-computed sequence alignments in diverse species * From 1 or 2 sequences of interacting partners: ** build 2 multiple sequence alignments with the same species ordered in each ** query the InterEvol database with alignments using profile-profile comparison method * Visualize structure vs sequence alignment at the complex interface ** A dedicated Pymol plugin is provided ** Alignment views in Pymol are interactively restricted to the residues selected at the interface

Proper citation: InterEvol database (RRID:SCR_006054) Copy   

•   Source: SciCrunch Registry

http://ucsd.researchaccelerator.org/

Software platform that allows researchers to easily collaborate on research and share reagents, antibodies, cell lines and more. It is designed to increase scientific collaboration across disciplines and geographical boundaries. Among the institutions now using the platform include Yale University, U of Pennsylvania, U of Chicago, Washington U, Cambridge University, University College London. The platform is licensed to select institutions. ResearchAccelerator.org allows researchers to form targeted, data driven collaborations. Researchers can search for data based on gene, disease and pathway, and they can post data which would otherwise be orphaned. The resulting collaborations, which are likely to be transdisciplinary, can greatly amplify impact and research productivity.

Proper citation: Research Accelerator (RRID:SCR_006051) Copy   

•   Source: SciCrunch Registry

http://www.umass.edu/

A campus of the University of Massachusetts system, located in Pioneer Valley of Western Massachusetts.

Proper citation: University of Massachusetts Amherst; Massachusetts; USA (RRID:SCR_006052) Copy   

•   Source: SciCrunch Registry

http://syndb.cbi.pku.edu.cn

SynDB is an online resource of proteins known or predicted to be related to the synapse or synaptic activity, and extensive information on the proteins'' functions, sequences, structures, expression, pathways, interactions, and disease associations. It is intended to be a repository of current knowledge and data as well as a starting point for future proteomics research in neurobiology. SynDB is the first focused database of the molecular biology of the synapse proteome. It contains the most comprehensive collection of proteins (13809 unique proteins spanning 1979 species and 104 protein domains, Aug 2006) that are known or predicted to be associated with synaptic activities. It integrates extensive information on protein functions, sequences, structures, expression, pathways, interactions, and disease associations. SynDB was generated using a combination of automated approaches, including keyword- and domain-based searches, and manual curation. It serves as a starting point for future neurobiology, neuropharmacology, and neuroinformatics research. Synapse ontology is a set of standard vocabulary which help to describe all synaptic gene products in a consistant way. As in common ontology, synapse ontolgy is composed of all the terms in a hierarchical structure, but specifically restricted to the function and structure annotation of synapse related gene products. Synapse ontology is a callaborative fruit of bioinformatists and neural biologists. Synapse ontolgy is aimed to describe all the synaptic molecules in terms of structure/biochemistry of synapse and physiology/function at synapse in a specied-independent manner. The controled vocabularies are hierarchically structured, so you can browser the related gene products in different levels: for example, you can find all the gene products of synaptic vesicle cycling or ion channels and receptors, or you can zoom in on all the gene products playing roles in the priming step of synaptic vesicle cycling.

Proper citation: SynDB: Synapse DataBase (RRID:SCR_005918) Copy   

•   Source: SciCrunch Registry