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The TRIPOS filing machine, a front end to a file server

M. F. Richardson, R. M. Needham
1983 Proceedings of the ninth ACM symposium on Operating systems principles - SOSP '83  
First, there is great advantage to be gained from having e front end to a file server that takes advantage of knowledge of the patterns of use expected of a particular subset of the file server's clients  ...  It would be comparatively easy to provide further services analogous to the TRIPOS filing machine, for example a data-base server.  ... 
doi:10.1145/800217.806620 dblp:conf/sosp/RichardsonN83 fatcat:wj7nhsrwbjdlfk3ro3bqcjjluy

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

Enguerran Vanquelef, Sabrina Simon, Gaelle Marquant, Elodie Garcia, Geoffroy Klimerak, Jean Charles Delepine, Piotr Cieplak, François-Yves Dupradeau
2011 Nucleic Acids Research  
Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format.  ...  Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.  ...  Dupradeau is grateful to Alineos SA (Linux solutions provider for high-performance numerical computation, Bourron-Marlotte, France) for supporting R.E.D. Server. P.  ... 
doi:10.1093/nar/gkr288 pmid:21609950 pmcid:PMC3125739 fatcat:tw5xcrb4wjgqfkhsdackoz2rzm

Distributed operating systems

Andrew S. Tanenbaum, Robbert Van Renesse
1985 ACM Computing Surveys  
This paper is intended as an introduction to distributed operating systems, and especially to current university research about them.  ...  After a discussion of what constitutes a distributed operating system and how it is distinguished from a computer network, various key design issues are discussed.  ...  ACKNOWLEDGMENTS We would like to thank Andrew Black, Dick Grune, Sape Mullender, and Jennifer Steiner for their critical reading of the manuscript.  ... 
doi:10.1145/6041.6074 fatcat:mpv2guiqsvf6zi26h7hh5xqdkm

A Generalized Framework for Biological Data Integration, Processing and Visualization

Rauf Ahmed Shams Malick Muhammad Ussama
2013 Journal of Information Technology & Software Engineering  
The present study is an effort towards seamless integration of heterogeneous data bases with a complexity of analysis and varieties in its presentation formats.  ...  This paper presents an experience of a unified framework development which combines complex input module with massive processing methods in a collaborative visualization environment.  ...  The server machine will be responsible to delegate the views to all the participants of the session.  ... 
doi:10.4172/2165-7866.1000115 fatcat:elo63adugza7zmwaoqkuii52ia

Mordred: a molecular descriptor calculator

Hirotomo Moriwaki, Yu-Shi Tian, Norihito Kawashita, Tatsuya Takagi
2018 Journal of Cheminformatics  
Mordred can be easily installed and used in the command line interface, as a web application, or as a high-flexibility Python package on all major platforms (Windows, Linux, and macOS).  ...  Owing to its good performance, convenience, number of descriptors, and a lax licensing constraint, Mordred is a promising choice of molecular descriptor calculation software that can be utilized for cheminformatics  ...  We would like to thank Editage ( for English language editing.  ... 
doi:10.1186/s13321-018-0258-y pmid:29411163 pmcid:PMC5801138 fatcat:ihrb2p5vwvhjzoakuaqe27bjn4

CancerHSP: anticancer herbs database of systems pharmacology

Weiyang Tao, Bohui Li, Shuo Gao, Yaofei Bai, Piar Ali Shar, Wenjuan Zhang, Zihu Guo, Ke Sun, Yingxue Fu, Chao Huang, Chunli Zheng, Jiexin Mu (+4 others)
2015 Scientific Reports  
of complexity ranging from molecular and cellular levels to tissue and organism levels, leading to a new opportunity to overcome these obstacles 9,10 .  ...  However, pharmacokinetics (the absorption, distribution, metabolism, and excretion (ADME) properties of a drug) and targets of these products were seldom fully evaluated owing to the time consuming and  ...  (b) The front end is a web interface based on HTML, CSS, PHP and JavaScript programming languages.Scientific RepoRts | 5:11481 | DOi: 10.1038/srep11481  ... 
doi:10.1038/srep11481 pmid:26074488 pmcid:PMC4466901 fatcat:mtnaxkbgsbajbmi3qu2cepy4s4

VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface

Álvaro Cortés Cabrera, Rubén Gil-Redondo, Almudena Perona, Federico Gago, Antonio Morreale
2011 Journal of Computer-Aided Molecular Design  
We also show that by combining LBVS and SBVS, and using a cluster of *100 modern processors, it is possible to perform complete VS studies of several million molecules in less than a month.  ...  In addition, a ligandbased VS module (LBVS) has been implemented that complements the already existing structure-based VS (SBVS) module and can be used in those cases where the receptor's 3D structure  ...  Acknowledgments The authors thank Dr. Eva M a Priego and Dr.  ... 
doi:10.1007/s10822-011-9465-6 pmid:21826555 fatcat:fyqw2iegqrbrbm5xzvn55kazgu

Workflow Tools for Managing Biological and Chemical Data [chapter]

Thorsten Meinl, Bernd Wiswedel, Michael R. Berthold
2011 Computational Approaches in Cheminformatics and Bioinformatics  
Spe-CIal thanks goes to NycomeaAor t~e vHTS and cell imacre data used in ~he example flows. Last but not least, Heathl r Fyson didO a great job of Improving readability and spelling.  ...  Acknowledgments We want to thank the members in our group who have provided valuable comments while preparing this chapter (besides having implemented various parts Of.  ...  Taverna is being developed as part of the UK's myGrid initiative. 2 ! Its main focus is on using independent Web services via a common workflow-oriented front end.  ... 
doi:10.1002/9781118131411.ch7 fatcat:swyn6fwrurctzo5vpr3s7444am

Chemical Informatics and the Drug Discovery Knowledge Pyramid

Gerald Lushington, Yinghua Dong, Bhargav Theertham
2013 Combinatorial chemistry & high throughput screening  
so as to enhance the likelihood that users will be able to extract meaningful information from data queries.  ...  The magnitude of the challenges in preclinical drug discovery is evident in the large amount of capital invested in such efforts in pursuit of a small static number of eventually successful marketable  ...  to be implemented for front-end analysis) and developing a hardware specification (e.g., number and speed of CPUs, amount of memory and storage, etc.) that somewhat exceeds the currently anticipated requirements  ... 
doi:10.2174/1386207311301010006 pmid:23782037 pmcid:PMC3796186 fatcat:aevfl5rh2bbjta4sob6atu3sla

PubChem chemical structure standardization

Volker D. Hähnke, Sunghwan Kim, Evan E. Bolton
2018 Journal of Cheminformatics  
It is worth noting that 60% of the structures obtained from PubChem structure standardization are not identical to the chemical structure resulting from the InChI (primarily due to preferences for a different  ...  Furthermore, the PubChem standardization is compared to the structure normalization of the IUPAC International Chemical Identifier (InChI) software, as manifested by conversion of the InChI back into a  ...  the term 'RoboChemistry' , as well as Paul Thiessen (NCBI-NLM-NIH) for providing an interface to the InChI library made available by the InChI Trust.  ... 
doi:10.1186/s13321-018-0293-8 pmid:30097821 pmcid:PMC6086778 fatcat:znp7oqltlfdorp5hxr2n6cuog4

Software and resources for computational medicinal chemistry

Chenzhong Liao, Markus Sitzmann, Angelo Pugliese, Marc C Nicklaus
2011 Future Medicinal Chemistry  
Drug discovery and development is a very costly and time-consuming process in which every available discipline, including computer-aided drug design (CADD), is utilized in order to achieve the desired  ...  focus on, and subsequently become an expert in, the use of just one or a few specific techniques.  ...  In particular, VMD can act as a graphical front-end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. • Molecular Networks GmbH [240]: provides  ... 
doi:10.4155/fmc.11.63 pmid:21707404 pmcid:PMC3413324 fatcat:csjirmoxcfhntfhgirqdm3hjae

Dr. Hertoghe on Thyroid Deficiency, John Henry Poynting, and more

1914 Scientific American  
1897, in which a rotary pump connects mantel is prolonged by carrying the burn with the two ends of the power cylinder er on springs ; the Fuller patent, 580,126, and pumps the water from one end of the  ...  I t carries, in front, trigger pins and percussion caps separated by an in terspace, and having well to the rear an ignition cha rge.  ... 
doi:10.1038/scientificamerican05021914-378 fatcat:txcqlxdhazehvpsonycxknwlfm

The role of exception mechanisms in software systems design

Margaret Stella Atkins
notification from a server to its client or clients.  ...  Server-to-client exceptions are of particular interest because of their ubiquity; these are exceptions detected by a server and handled by a client.  ...  Starting with this view, the exceptions to recognize are END-OF-FILE, a server-client exception, and a BACKSPACE, a peer exception transparent to the user.  ... 
doi:10.14288/1.0051908 fatcat:pqvnh6sa4jbhxfilkrncl4zxqu

Other Related Techniques [chapter]

Kunal Roy, Supratik Kar, Rudra Narayan Das
2015 Understanding the Basics of QSAR for Applications in Pharmaceutical Sciences and Risk Assessment  
will play the front-runner role in drug design in the near future either as a complementary approach to HTS or as a stand-alone approach.  ...  available from Tripos Inc.  ... 
doi:10.1016/b978-0-12-801505-6.00010-7 fatcat:s3cwmvwklngdfdcwjb4vnqejci

Phylogenetic Analysis [chapter]

An Introduction to Computational Biochemistry  
Access is provided through a local host or news server machine. Telnet. Telnet is a program using the communication protocol of the Internet (TCP/IP) to provide a connection onto remote computers.  ...  A procedure language such as FORTRAN and C enables a programmer to communicate with many different machines in the same language, and it is easier to comprehend than machine language.  ...  Retrieve nucleotide sequence (fasta file) and atomic coordinates (pdb file) of yeast Asp-tRNA.  ... 
doi:10.1002/0471223840.ch13 fatcat:nipg4bxrevau3efb6bagqscufy
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