Software pipelines

Below we briefly describe the crystallographic software pipelines using AutoRickshaw as an example, with its flexibility and the ability to decide on the path to be taken dependent on the outcome of a previous step. On one hand, AutoRickshaw has features and general steps, which are also shared by many other pipelines. On the other hand, AutoRickshaw is perhaps the first software pipeline which aims not at the delivery of a fully built, refined, and validated model but rather at fast evaluation of the quality of the X-ray data in terms of interpretability of the obtained electron density map. 

In the present, work for hydrate formation prediction a well known numerical simulation software (Pipeline Studio-TGNET) is employed [2]. In addition, to calibrate the model, the results of an experiment carried out in a part of Tehran gas network are used. Some research works related to hydrate formation and numerical simulation of natural gas flow in a network can be found in [3-6]. 

Arzhaev A T, Bougaenko S E., Denisov I N., Aladinsky V V, Makhanev V.O. Technical basis and software development for flaw assessments in NPP pipeline welds. In Ageing of Materials andMethods for the Assessment of Lifetimes of Engineering Plant, R.K. Penny (Ed ), 1997, pp. 63-68. 

Many developers of software for finite-element analysis (18) provide drafting of pipelines and associated flow analysis. These companies include Algor, McAuto, MacNeal-Schwindler, and ElowDesign. In software, in-house developed pipe fittings are modularized and isometric views of the piping systems with three-dimensional detailing are now commonplace. 

More recently, the Southern Gas Association s Gas Machinery Research Council and Pipeline and Compressor Research Council cooperated with Southwest Research Institute to develop a software package that enhances reciprocating compressor operation. Several major American and foreign compressor manufacturers (and some other interested companies) have cooperated with Southwest Research Institute or developed their own proprietary pulsation-reduction design computer programs. 

Ultimately, software is bought to accomplish a business result. Therefore, software offerings in pharmaceutical R D ought to somehow accelerate R D productivity, or at least give cost savings along the pipeline. Yet the reality is that most scientific software is not sold on the basis of delivering... 

The pragmatic beauty of the chemical fingerprint is that the more common features of two molecules that there are, the more common bits are set. The mathematic approach used to translate the fingerprint comparison data into a measure of similarity tunes the molecular comparison [5]. The Tanimoto similarity index works well when a relatively sparse fingerprint is used and when the molecules to be compared are broadly comparable in size and complexity [5]. If the nature of the molecules or the comparison desired is not adequately met by the Tanimoto index, multiple other indices are available to the researcher. For example, the Daylight software offers the user over ten similarity metrics, and the Pipeline Pilot as distributed offers at least three. Some of these metrics (e.g., Tversky, Cosine) offer better behavior if the query molecule is significantly smaller than the molecule compared to it. 

Figure 6. Distributions of essential computed molecular properties defining drug-likeness for selected compound sets. Shown are the fraction of compounds vs. the properties. Orange NIBR historical medicinal chemistry collection. Brown Compilation of combinatorial chemistry libraries. Dark Green Drugs (launched or Phase III listed in MDDR or CMC). Brown Compilation from combinatorial libraries. Pink Natural products of DNP. tight Green HTS hits of NIBR 2004 screens. All properties were calculated with Pipeline Pilot software www.scitegic.com).

Figure 7. Multiclass NaTve Bayes modeling within Pipeline Pilot software (www.scitegic.com) based on the WOMBAT chemogenomics dataset Probabilistic target predictions are possible for compounds given only their chemical structure. In the example shown, the WOMBAT targets were predicted for Calphostin C, a known protein kinase C inhibiting natural product Tubulin and beta-hexosaminidase are predicted as additional possible targets.

Figure 7 shows the web interface for our Pipeline Pilot-based similarity search engine. For similarity searching a connectivity fingerprint (available within the Pipeline Pilot software) is used and the Tanimoto coefficient is calculated. In the text box (labeled JNJNumberList under Parameters ) one can type or paste (e.g., from an Excel sheet) a list of identification numbers ( jnjnumber, batchid ) to be used as probes for the search. Alternatively, an... 

Includes the software programs CSMGem, which supplies the most recent thermodynamic predictions, and CSMPlug, which provides the time required for hydrate plug removal from a pipeline... 

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