Abstract: A portable access point device is formed from a handheld computing device; an environmentally hardened case disposed around the computing device, and an access point module for reading and writing data to low frequency active radiating transceiver tags, such as RuBee® tags. The access point module is connected to the handheld computing device and the environmentally hardened case to provide a unitary handheld device, and the access point module transfers data between the handheld computing device and tags within communication range of the device.

Abstract: A system has tags communicating by means of low frequency (below 1 megahertz) with routers which in turn communicate with nameservers. The tags have IP addresses, either explicitly programmed into the tags or associated in a virtual way with the tags. Lookups analogous to domain lookups permit human-friendly inquiries of tag status and location. Static (battery-backed) RAM in a tag permits great versatility in the localized function of the tag.

Abstract: Data traces from four channels of an automated electrophoresis detection apparatus are aligned by identifying peaks in each of the four data traces; optionally normalizing the data traces to achieve a uniform peak height; combining the four data traces in an initial alignment; and determining coefficients of shift and stretch for selected data points within each data trace. The coefficients are determined by optimizing a cost function which reflects the extent of overlap of peaks in the combined normalized data traces to which the coefficients have been applied. The cost function is optimized when the extent of overlap is at a minimum. The coefficients are then used to generate a warp function for each data trace. These warp functions are applied to their respective data traces to produce four warped data traces which are aligned to form an aligned data set. The aligned data set may be displayed on a video screen of a sequencing apparatus, or may be used as the data set for a base-calling process.

Abstract: Nucleic acid polymers are sequenced by obtaining forward and reverse data sets for forward and reverse strands of a sample nucleic acid polymer. The apparent base sequences of these forward and reverse sets are determined and the apparent sequences are compared to identify any deviations from perfect complementarity. Any such deviation presents a choice between two bases, only one of which is correct. A confidence algorithm is applied to the peaks in the data sets associated with a deviation to arrive at a numerical confidence value for each of the two base choices. These confidence values are compared to each other and to a predetermined threshold, and the base represented by the peak with the better confidence value is assigned as the “correct” base, provided that its confidence value is better than the threshold. The confidence value takes into account at least one, and preferably more than one of several specific characteristics of the peaks in the data set that were not complementary.

Abstract: Normalization of experimental fragment patterns for nucleic acid polymers having putatively known sequences starts with obtaining at least one raw fragment pattern for the experimental sample. The raw fragment pattern represents the positions of a selected nucleic acid base within the polymer as a function of migration time or distance. This raw fragment pattern is conditioned using conventional baseline correction and noise reduction technique to yield a clean fragment pattern. The clean fragment pattern is then evaluated to determine one or more “normalization coefficients.

Abstract: Electrophoretic separation of an analyte species in a sample is achieved with increased resolution by loading the sample onto a loading site of an electrophoresis gel, said loading site having a gel/buffer interface and then applying a focusing electric field to a first pair of electrodes to cause the analyte species to migrate to a narrow region disposed at or near the loading site to produce a focused sample. Then a separation electric field is applied to cause the analyte species in the focused sample to migrate through the electrophoresis gel and to be separated into bands. This method is preferably performed in an electrophoresis apparatus that is particularly adapted to practicing the method by virtue of the a pair of focusing electrodes which are positioned to cause migration of sample to a narrow region near the buffer/gel interface within the sample loading site of the gel.

Abstract: The sequence of a target nucleic acid polymer can be determined by (a) performing a first chain-extension sequencing reaction on the target nucleic acid polymer in a reaction mixture containing first and second chain-terminators to produce a first product mixture containing commonly-labeled polynucleotide fragments complementary to a first strand of the target nucleic acid polymer, each fragment in the mixture being terminated with the first or second chain-terminator; (b) performing a second chain extension sequencing reaction on the target nucleic acid polymer in a reaction mixture containing the first and a third chain-terminator to produce a second product mixture containing commonly-labeled polynucleotide fragments complementary to the first strand of the target nucleic acid polymer, each fragment in the mixture being terminated with the first or the third chain-terminator, said first, second and third chain-terminators each being different; and (c) evaluating the lengths of the polynucleotide fragments

Abstract: Data traces from four channels of an automated electrophoresis detection apparatus are aligned by identifying peaks in each of the four data traces; normalizing the heights of the peaks in each of the data traces to a common value to generate four normalized data traces; combining the four normalized data traces in an initial alignment; and determining coefficients of shift and stretch for selected data points within each normalized data trace. The coefficients are determined by optimizing a cost function which reflects the extent of overlap of peaks in the combined normalized data traces to which the coefficients have been applied. The cost function is optimized when the extent of overlap is at a minimum. The coefficients are then used to generate a warp function for each normalized data trace. These warp function are applied to their respective data traces to produce four warped data traces which are aligned to form an aligned data set.

Abstract: Normalization of experimental fragment patterns for nucleic acid polymers having putatively known sequences starts with obtaining at least one raw fragment pattern for the experimental sample. The raw fragment pattern represents the positions of a selected nucleic acid base within the polymer as a function of migration time or distance. This raw fragment pattern is conditioned using conventional baseline correction and noise reduction technique to yield a clean fragment pattern. The clean fragment pattern is then evaluated to determine one or more "normalization coefficients.