Ryan J. Farris

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The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new analysis(More)
The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic framework for these data. Updated monthly, these services are made available through the RDP-II website (http://rdp.cme.msu.edu/). RDP-II release 9.21 (August 2004)(More)
The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences (trees) derived from these data. RDP-II release 8.1 contains 16 277(More)
The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [Nucleic Acids Res. (2000), 28, 173-174], continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 8.0 (June 1, 2000) consisted of 16 277 aligned prokaryotic small subunit (SSU) rRNA sequences while the number of(More)
Substantial new features have been implemented at the Ribosomal Database Project in response to the increased importance of high-throughput rRNA sequence analysis in microbial ecology and related disciplines. The most important changes include quality analysis, including chimera detection, for all available rRNA sequences and the introduction of myRDP(More)
A hybrid functional electrical stimulation (FES)/orthosis system is being developed which combines two channels of (surface-electrode-based) electrical stimulation with a computer-controlled orthosis for the purpose of restoring gait to spinal cord injured (SCI) individuals (albeit with a stability aid, such as a walker). The orthosis is an energetically(More)
This paper presents an assessment of a lower limb exoskeleton for providing legged mobility to people with paraplegia. In particular, the paper presents a single-subject case study comparing legged locomotion using the exoskeleton to locomotion using knee-ankle-foot orthoses (KAFOs) on a subject with a T10 motor and sensory complete injury. The assessment(More)
High-throughput sequencing of 16S rRNA genes has increased our understanding of microbial community structure, but now even higher-throughput methods to the Illumina scale allow the creation of much larger datasets with more samples and orders-of-magnitude more sequences that swamp current analytic methods. We developed a method capable of handling these(More)
This paper describes a powered lower-limb orthosis that is intended to provide gait assistance to spinal cord injured (SCI) individuals by providing assistive torques at both hip and knee joints. The orthosis has a mass of 12 kg and is capable of providing maximum joint torques of 40 Nm with hip and knee joint ranges of motion from 105° flexion to 30°(More)
This paper presents preliminary results on the development of a powered lower limb orthosis intended to provide legged mobility (with the use of a stability aid, such as forearm crutches) to paraplegic individuals. The orthosis contains electric motors at both hip and both knee joints, which in conjunction with ankle-foot orthoses, provides appropriate(More)