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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
NASA NTRS1999

Improving the Unsteady Aerodynamic Performance of Transonic Turbines using Neural Networks

A recently developed neural net-based aerodynamic design procedure is used in the redesign of a transonic turbine stage to improve its unsteady aerodynamic performance. The redesign procedure used incorporates the advantages of both traditional response surface methodology and neural networks by employing a strategy called parameter-based partitioning of the design space. Starting from the reference design, a sequence of response surfaces based on both neural networks and polynomial fits are constructed to traverse the design space in search of an optimal solution that exhibits improved unsteady performance. The procedure combines the power of neural networks and the economy of low-order polynomials (in terms of number of simulations required and network training requirements). A time-accurate, two-dimensional, Navier-Stokes solver is used to evaluate the various intermediate designs and provide inputs to the optimization procedure. The procedure yielded a modified design that improves the aerodynamic performance through small changes to the reference design geometry. These results demonstrate the capabilities of the neural net-based design procedure, and also show the advantages of including high-fidelity unsteady simulations that capture the relevant flow physics in the design optimization process.

Rai, Man Mohan↗
NASA NTRS1998

Contrasting actions of pressor agents in severe autonomic failure

BACKGROUND: Orthostatic hypotension is the most disabling symptom of autonomic failure. The choice of a pressor agent is largely empiric, and it would be of great value to define predictors of a response. PATIENTS AND METHODS: In 35 patients with severe orthostatic hypotension due to multiple system atrophy or pure autonomic failure, we determined the effect on seated systolic blood pressure (SBP) of placebo, phenylpropanolamine (12.5 mg and 25 mg), yohimbine (5.4 mg), indomethacin (50 mg), ibuprofen (600 mg), caffeine (250 mg), and methylphenidate (5 mg). In a subgroup of patients, we compared the pressor effect of midodrine (5 mg) with the effect of phenylpropanolamine (12.5 mg). RESULTS: There were no significant differences in the pressor responses between patients with multiple system atrophy or pure autonomic failure. When compared with placebo, the pressor response was significant for phenylpropanolamine, yohimbine, and indomethacin. In a subgroup of patients, we confirmed that this pressor effect of phenylpropanolamine, yohimbine, and indomethacin corresponded to a significant increase in standing SBP. The pressor responses to ibuprofen, caffeine, and methylphenidate were not significantly different from placebo. Phenylpropanolamine and midodrine elicited similar pressor responses. There were no significant associations between drug response and autonomic function testing, postprandial hypotension, or plasma catecholamine levels. CONCLUSIONS: We conclude that significant increases in systolic blood pressure can be obtained in patients with orthostatic hypotension due to primary autonomic failure with phenylpropanolamine in low doses or yohimbine or indomethacin in moderate doses. The response to a pressor agent cannot be predicted by autonomic function testing or plasma catecholamines. Therefore, empiric testing with a sequence of medications, based on the risk of side effects in the individual patient and the probability of a response, is a useful approach.

Clinical Trial↗
NASA NTRS2006

Mapping of Technological Opportunities-Labyrinth Seal Example

All technological systems evolve based on evolutionary sequences that have repeated throughout history and can be abstracted from the history of technology and patents. These evolutionary sequences represent objective patterns and provide considerable insights that can be used to proactively model future seal concepts. This presentation provides an overview of how to map seal technology into the future using a labyrinth seal example. The mapping process delivers functional descriptions of sequential changes in market/consumer demand, from today s current paradigm to the next major paradigm shift. The future paradigm is developed according to a simple formula: the future paradigm is free of all flaws associated with the current paradigm; it is as far into the future as we can see. Although revolutionary, the vision of the future paradigm is typically not immediately or completely realizable nor is it normally seen as practical. There are several reasons that prevent immediate and complete practical application, such as: 1) Some of the required technological or business resources and knowledge not being available; 2) Availability of other technological or business resources are limited; and/or 3) Some necessary knowledge has not been completely developed. These factors tend to drive the Total Cost of Ownership or Utilization out of an acceptable range and revealing the reasons for the high Total Cost of Ownership or Utilization which provides a clear understanding of research opportunities essential for future developments and defines the current limits of the immediately achievable improvements. The typical roots of high Total Cost of Ownership or Utilization lie in the limited availability or even the absence of essential resources and knowledge necessary for its realization. In order to overcome this obstacle, step-by-step modification of the current paradigm is pursued to evolve from the current situation toward the ideal future, i.e., evolution rather than revolution. A key point is that evolutionary stages are mapped to show step-by-step evolution from the current paradigm to the next major paradigm.

Clarke, Dana W., Sr.↗
NASA NTRS2007

Visualization of Concurrent Program Executions

Various program analysis techniques are efficient at discovering failures and properties. However, it is often difficult to evaluate results, such as program traces. This calls for abstraction and visualization tools. We propose an approach based on UML sequence diagrams, addressing shortcomings of such diagrams for concurrency. The resulting visualization is expressive and provides all the necessary information at a glance.

concurrent programs↗
NASA NTRS2011

Post-Flight Microbial Analysis of Samples from the International Space Station Water Recovery System and Oxygen Generation System

The Regenerative, Environmental Control and Life Support System (ECLSS) on the International Space Station (ISS) includes the the Water Recovery System (WRS) and the Oxygen Generation System (OGS). The WRS consists of a Urine Processor Assembly (UPA) and Water Processor Assembly (WPA). This report describes microbial characterization of wastewater and surface samples collected from the WRS and OGS subsystems, returned to KSC, JSC, and MSFC on consecutive shuttle flights (STS-129 and STS-130) in 2009-10. STS-129 returned two filters that contained fluid samples from the WPA Waste Tank Orbital Recovery Unit (ORU), one from the waste tank and the other from the ISS humidity condensate. Direct count by microscopic enumeration revealed 8.38 x 104 cells per mL in the humidity condensate sample, but none of those cells were recoverable on solid agar media. In contrast, 3.32 x lOs cells per mL were measured from a surface swab of the WRS waste tank, including viable bacteria and fungi recovered after S12 days of incubation on solid agar media. Based on rDNA sequencing and phenotypic characterization, a fungus recovered from the filter was determined to be Lecythophora mutabilis. The bacterial isolate was identified by rDNA sequence data to be Methylobacterium radiotolerans. Additional UPA subsystem samples were returned on STS-130 for analysis. Both liquid and solid samples were collected from the Russian urine container (EDV), Distillation Assembly (DA) and Recycle Filter Tank Assembly (RFTA) for post-flight analysis. The bacterium Pseudomonas aeruginosa and fungus Chaetomium brasiliense were isolated from the EDV samples. No viable bacteria or fungi were recovered from RFTA brine samples (N= 6), but multiple samples (N = 11) from the DA and RFTA were found to contain fungal and bacterial cells. Many recovered cells have been identified to genus by rDNA sequencing and carbon source utilization profiling (BiOLOG Gen III). The presence of viable bacteria and fungi from WRS and OGS subsystems demonstrates the need for continued monitoring of ECLSS during future ISS operations and investigation of advanced antimicrobial controls.

Birmele, Michele N.↗
NASA NTRS2013

Flat Surface Damage Detection System (FSDDS)

The Flat Surface Damage Detection system (FSDDS} is a sensory system that is capable of detecting impact damages to surfaces utilizing a novel sensor system. This system will provide the ability to monitor the integrity of an inflatable habitat during in situ system health monitoring. The system consists of three main custom designed subsystems: the multi-layer sensing panel, the embedded monitoring system, and the graphical user interface (GUI). The GUI LABVIEW software uses a custom developed damage detection algorithm to determine the damage location based on the sequence of broken sensing lines. It estimates the damage size, the maximum depth, and plots the damage location on a graph. Successfully demonstrated as a stand alone technology during 2011 D-RATS. Software modification also allowed for communication with HDU avionics crew display which was demonstrated remotely (KSC to JSC} during 2012 integration testing. Integrated FSDDS system and stand alone multi-panel systems were demonstrated remotely and at JSC, Mission Operations Test using Space Network Research Federation (SNRF} network in 2012. FY13, FSDDS multi-panel integration with JSC and SNRF network Technology can allow for integration with other complementary damage detection systems.

Williams, Martha↗
NASA NTRS2015

Constraining the Texture and Composition of Pore-Filling Cements at Gale Crater, Mars

The Mars Science Laboratory (MSL) rover Curiosity has encountered a wide variety of sedimentary rocks deposited in fluvio-lacuestrine sequences at the base of Gale Crater. The presence of sedimentary rocks requires that initial sediments underwent diagenesis and were lithified. Lithification involves sediment compaction, cementation, and re-crystallization (or authigenic) processes. Analysis of the texture and composition of the cement can reveal the environmental conditions when the cements were deposited, enabling better understanding of early environments present within Gale Crater. The first step in lithification is sediment compaction. The Gale crater sediments do not show evidence for extensive compaction prior to cementation; the Sheepbed mudstone in Yellowknife Bay (YKB) has preserved void spaces ("hollow nodules"), indicating that sediments were cemented around the hollow prior to compaction, and conglomerates show imbrication, indicating minimal grain reorganization prior to lithification. Furthermore, assuming the maximum burial depth of these sediments is equivalent to the depth of Gale Crater, the sediments were never under more than 1 kb of pressure, and assuming a 15 C/km thermal gradient in the late Noachian, the maximum temperature of diagenesis would have been approximately 75 C. This is comparable to shallow burial diagenetic conditions on Earth. The cementation and recrystallization components of lithification are closely intertwined. Cementation describes the precipitation of minerals between grains from pore fluids, and recrystallization (or authigenesis) is when the original sedimentary mineral grains are altered into secondary minerals. The presence of authigenic smectites and magnetite in the YKB formation suggests that some recrystallization has taken place. The relatively high percentage of XRD-amorphous material (25-40%) detected by CheMin suggests that this recrystallization may be limited in scope, and therefore may not contribute significantly to the cementing material. However, relatively persistent amorphous components could exist in the Martian environment (e.g. amorphous MgSO4), so recrystallization, including loss of crystallinity, cannot yet be excluded as a method of cementation. In order to describe the rock cementation, both the rock textures and their composition must be considered. Here, we attempt to summarize the current understanding of the textural and compositional aspects of the cement across the rocks analyzed by Curiosity to this point.

Siebach, K. L.↗
NASA NTRSDate not supplied

Method Development for In Situ Microbiome Profiling of the Water Recovery System’s Wastewater Tank Onboard the International Space Station

A distinctive microbial community has inhabited the wastewater tank within the International Space Station Water Recovery System (WRS) for over 14 years and experienced the stressors associated with the microgravity environment. The WRS generates potable water for the crew from urine distillate, humidity condensate, Sabatier product water, and the occasional off-loading of ground-supplied water. The reservoir for these products, the wastewater tank, does not have a means of microbial control. While samples are occasionally collected for analysis, the time between sample collection and the return to Earth, as well as the lack of preservation, results in a skewed depiction of the microbiome. Routinely observed from these returned samples are high counts (105 – 106 colony forming units per mL) and two prevailing genera, Burkholderia and Ralstonia. The wastewater tank likely contains a more diverse microbiome, as a higher diversity of bacteria and fungus has been noted upstream and downstream of the tank. To characterize the microbial profile of the tank, analysis needs to occur at the time of sample collection. Toward this goal, a method for in situ analysis based on nanopore sequencing was developed. The filter-to-sequencer method evolved from previous work that has been validated onboard the ISS (BEST payload and the BioMole Crew Health Care Systems Facility). The method, including filtration, DNA extraction, purification, amplification, library preparation, and nanopore sequencing will be described. Additionally, data collected with this method from both ISS and terrestrial samples will be detailed. The consumables needed to support in situ analysis of the tank are set to the launch to the ISS in the spring of 2023. This investigation will allow for the first accurate characterization of the microbiome of the tank providing insight for crew health, planetary protection, and has the potential to enable engineering controls for future space station water systems.

Sarah Stahl-Rommel↗
DOE OSTI2016

Hypothesis-driven classification of materials using nuclear magnetic resonance relaxometry

Technologies related to identification of a substance in an optimized manner are provided. A reference group of known materials is identified. Each known material has known values for several classification parameters. The classification parameters comprise at least one of T.sub.1, T.sub.2, T.sub.1.rho., a relative nuclear susceptibility (RNS) of the substance, and an x-ray linear attenuation coefficient (LAC) of the substance. A measurement sequence is optimized based on at least one of a measurement cost of each of the classification parameters and an initial probability of each of the known materials in the reference group.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Method for instruction sequence execution analysis and visualization

Various technologies pertaining to computer-executable instruction sequence forensics are described herein. In a general embodiment, an application development framework supports a function library that includes a plurality of recording functions. Calls to these functions are inserted into source code or bytecode of the computer-executable instruction sequence. The source code is then compiled, resulting in formation of instrumented machine code of the computer-executable instruction sequence. Alternately, the runtime environment interprets instrumented bytecode for the instruction sequence. A processor executes the machine code, and the called functions cause the processor to generate forensic data pertaining to portions of the computer-executable instruction sequence that correspond to locations in the source code where the calls were inserted. An execution instance of the computer-executable instruction sequence is visualized based upon the forensic data.

Sundermier, Amy↗
DOE OSTI2020

Estimating the Timing of Early Simian-Human Immunodeficiency Virus Infections: a Comparison between Poisson Fitter and BEAST

Many HIV prevention strategies are currently under consideration where it is highly informative to know the study participants’ times of infection. These can be estimated using viral sequence data sampled early in infection. However, there are several scenarios that, if not addressed, can skew timing estimates. These include multiple transmitted/founder (TF) viruses, APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like)-mediated mutational enrichment, and recombination. Here, we suggest a pipeline to identify these problems and resolve the biases that they introduce. We then compare two modeling strategies to obtain timing estimates from sequence data. The first, Poisson Fitter (PF), is based on a Poisson model of random accumulation of mutations relative to the TF virus (or viruses) that established the infection. The second uses a coalescence-based phylogenetic strategy as implemented in BEAST. The comparison is based on timing predictions using plasma viral RNA (cDNA) sequence data from 28 simian-human immunodeficiency virus (SHIV)-infected animals for which the exact day of infection is known. In this particular setting, based on nucleotide sequences from samples obtained in early infection, the Poisson method yielded more accurate, more precise, and unbiased estimates for the time of infection than did the explored implementations of BEAST. The inference of the time of infection is a critical parameter in testing the efficacy of clinical interventions in protecting against HIV-1 infection. For example, in clinical trials evaluating the efficacy of passively delivered antibodies (Abs) for preventing infections, accurate time of infection data are essential for discerning levels of the Abs required to confer protection, given the natural Ab decay rate in the human body. In such trials, genetic sequences from early in the infection are regularly sampled from study participants, generally prior to immune selection, when the viral population is still expanding and genetic diversity is low. In this particular setting of early viral growth, the Poisson method is superior to the alternative approach based on coalescent methods. This approach can also be applied in human vaccine trials, where accurate estimates of infection times help ascertain if vaccine-elicited immune protection wanes over time.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Comparative genomics analysis of Trichoderma reesei strains

Trichoderma reesei is a key fungus for industrial production of lignocellulolytic enzymes. The genome sequences of the Trichoderma reesei hyper-cellulolytic strain RUT-C30 and its parental strain QM6a were compared at the nucleotide level. Approximately 97 % of the 87 genomic sequence scaffolds of T. reesei QM6a (33Mb) were detected to have the correspondent nucleotide in the 182 genome sequence scaffolds of RUT-C30 (32Mb). There are 455 loci within the QM6 sequence not detected in the RUT-C30 sequence. Regions at the termini of QM6a scaffolds as well as 14 small scaffolds do not have corresponding regions in RUT-C30 genomic scaffolds. Seventy-eight protein encoding genes are included within these regions. Mutated nucleotide(s) in 2,371 positions, including short insertion/deletions (indels) were detected in the aligned regions. The predicted protein coding regions of 97 gene models contain mutations, 34 of which were not previously described. Twenty-seven out of 34 newly discovered genes were found to have mutations in the peptide amino acid sequence. This is in addition to 63 genes described in a previous study based on low coverage sequencing of RUT-C30. These newly identified proteins are involved in signal transduction, transcription, RNA processing and modification, post-translational modification according to their annotations. Similar distributions of eukaryotic orthologous group (KOG) categories between the mutated and all other proteins suggest random mutation. The roles of the mutated genes and potential regulatory regions in the observed phenotype of RUT-C30 remain to be explored in a targeted fashion.

Trichoderma, genomics, biofuels, enzymes, cellulas↗
NASA NTRS1987

Use of a FORTH-based PROLOG for real-time expert systems. 1: Spacelab life sciences experiment application

A real-time expert system is being developed to serve as the astronaut interface for a series of Spacelab vestibular experiments. This expert system is written in a version of Prolog that is itself written in Forth. The Prolog contains a predicate that can be used to execute Forth definitions; thus, the Forth becomes an embedded real-time operating system within the Prolog programming environment. The expert system consists of a data base containing detailed operational instructions for each experiment, a rule base containing Prolog clauses used to determine the next step in an experiment sequence, and a procedure base containing Prolog goals formed from real-time routines coded in Forth. In this paper, we demonstrate and describe the techniques and considerations used to develop this real-time expert system, and we conclude that Forth-based Prolog provides a viable implementation vehicle for this and similar applications.

Paloski, William H.↗
DOE OSTI2017

Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline

The dinitrogenase reductase gene ( nifH ) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. Furthermore, the developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field. IMPORTANCE: Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. Thus, the utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Sponge exhalent metabolites influence coral reef picoplankton dynamics

Coral reef sponges efficiently take up particulate and dissolved organic matter (DOM) from the water column and release compounds such as nucleosides, amino acids, and other dissolved metabolites to the surrounding reef via their exhalent seawater, but the influence of this process on reef picoplankton and nutrient processing is relatively unexplored. Here we examined the impact of sponge exhalent on the reef picoplankon community and subsequent alterations to the reef dissolved metabolite pool. We exposed reef picoplankton communities to a sponge exhalent water mixture (Niphates digitalis and Xestospongia muta) or filtered reef seawater (control) in closed, container-based dark incubations. We used 16S rRNA gene sequencing and flow cytometry-based cell counts to examine the picoplankton community and metabolomics and other analyses to examine the dissolved metabolite pool. The initial sponge exhalent was enriched in adenosine, inosine, chorismate, humic-like and amino acid-like components, and ammonium. Following 48 h of exposure to sponge exhalent, the picoplankton differed in composition, were reduced in diversity, showed doubled (or higher) growth efficiencies, and harbored increased copiotrophic and denitrifying taxa (Marinomonas, Pontibacterium, Aliiroseovarius) compared to control, reef-water based incubations. Alongside these picoplankton alterations, the sponge treatments, relative to seawater controls, had decreased adenosine, inosine, tryptophan, and ammonium, metabolites that may support the observed higher picoplankton growth efficiencies. Sponge treatments also had a net increase in several monosaccharides and other metabolites including anthranilate, riboflavin, nitrite, and nitrate. Our work demonstrates a link between sponge exhalent-associated metabolites and the picoplankton community, with exhalent water supporting an increased abundance of efficient, copiotrophic taxa that catabolize complex nutrients. The copiotrophic taxa were often different from those observed in previous algae and coral studies. These results have implications for better understanding the multifaceted role of sponges on picoplankton biomass with subsequent potential impacts to coral and other planktonic feeders in oligotrophic reef environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures

Aptamers can be highly specific for their targets, which implies precise molecular recognition between aptamer and target. However, as small polymers, their structures are more subject to environmental conditions than the more constrained longer RNAs such as those that constitute the ribosome. To understand the balance between structural and environmental factors in establishing ligand specificity of aptamers, we examined the RNA aptamer (NEO1A) previously reported as specific for neomycin-B. We show that NEO1A can recognize other aminoglycosides with similar affinities as for neomycin-B and its aminoglycoside specificity is strongly influenced by ionic strength and buffer composition. NMR and 2-aminopurine (2AP) fluorescence studies of the aptamer identified a flexible pentaloop and a stable binding pocket. Consistent with a well structured binding pocket, docking analysis results correlated with experimental measures of the binding energy for most ligands. Steady state fluorescence studies of 2AP-substituted aptamers confirmed that A16 moves to a more solvent accessible position upon ligand binding while A14 moves to a less solvent accessible position, which is most likely a base stack. Analysis of binding affinities of NEO1A sequence variants showed that the base in position 16 interacts differently with each ligand and the interaction is a function of the buffer constituents. Our results show that the pentaloop provides NEO1A with the ability to adapt to external influences on its structure, with the critical base at position 16 adjusting to incorporate each ligand into a stable pocket by hydrophobic interactions and/or hydrogen bonds depending on the ligand and the ionic environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Combining de novo and reference-guided assembly with scaffold_builder

Genome sequencing has become routine, however genome assembly still remains a challenge despite the computational advances in the last decade. In particular, the abundance of repeat elements in genomes makes it difficult to assemble them into a single complete sequence. Identical repeats shorter than the average read length can generally be assembled without issue. However, longer repeats such as ribosomal RNA operons cannot be accurately assembled using existing tools. The application Scaffold_builder was designed to generate scaffolds – super contigs of sequences joined by N-bases – based on the similarity to a closely related reference sequence. This is independent of mate-pair information and can be used complementarily for genome assembly, e.g. when matepairs are not available or have already been exploited. Scaffold_builder was evaluated using simulated pyrosequencing reads of the bacterial genomes Escherichia coli 042, Lactobacillus salivarius UCC118 and Salmonella enterica subsp. enterica serovar Typhi str. P-stx-12. Moreover, we sequenced two genomes from Salmonella enterica serovar Typhimurium LT2 G455 and Salmonella enterica serovar Typhimurium SDT1291 and show that Scaffold_builder decreases the number of contig sequences by 53% while more than doubling their average length. Scaffold_builder is written in Python and is available at http://edwards.sdsu.edu/scaffold_builder. A web-based implementation is additionally provided to allow users to submit a reference genome and a set of contigs to be scaffolded.

Salmonella enterica serovar typhimurium↗