A simple polymerase chain reaction apparatus based on a computer printer.

We describe a very simple laboratory-made polymerase chain reaction (PCR) apparatus. The reaction tubes are placed in a holder fixed through a mechanical arm to the tape cartridge of a computer printer. A computer controls the horizontal movement of the tube carrier by sending the proper printing commands. The holder is raised or lowered by a frame fixed to the paper-advancing roller of the printer. The system allows the programmed movement of the test tubes within the holder, successively through three thermal baths placed in front of the printer. DNA from single lambda gtll lysis plaques was successfully amplified with this system in our laboratory.     

Profile sequence analysis and database searches on a transputer machine connected to a Macintosh computer

An implementation of Profilesearch (a technique to search forrelationships between a protein sequence and multiply alignedsequences) for a parallel computer is described. The numbercrunchingmachine, consisting of 21 T800 transputers, is connected toa Macintosh IIcx host computer. The program utilizes a standardMacintosh application as its user–interface, resultingin a transparent and user–friendly environment for addressingthe parallel computer. The program is independent of the nwnberof available processors and exceeds the speed of a VAXstation3200 with only one transputer in operation, thus allowing cheapand fast database searches with a PC frontend. For a largernwnber of processors, the speed increase is approximately linearwith no obvious symptoms of saturation with the available maximwnof 21 transputers. The program and environment are usefid tosearch quickly and easily for similarities between a singlesequence or sequence set and individual sequences containedin a large database. The alignment is determined by typicaldynamic programming techniques.     

Open-Source Syringe Pump Library

This article explores a new open-source method for developing and manufacturing high-quality scientific equipment suitable for use in virtually any laboratory. A syringe pump was designed using freely available open-source computer aided design (CAD) software and manufactured using an open-source RepRap 3-D printer and readily available parts. The design, bill of materials and assembly instructions are globally available to anyone wishing to use them. Details are provided covering the use of the CAD software and the RepRap 3-D printer. The use of an open-source Rasberry Pi computer as a wireless control device is also illustrated. Performance of the syringe pump was assessed and the methods used for assessment are detailed. The cost of the entire system, including the controller and web-based control interface, is on the order of 5% or less than one would expect to pay for a commercial syringe pump having similar performance. The design should suit the needs of a given research activity requiring a syringe pump including carefully controlled dosing of reagents, pharmaceuticals, and delivery of viscous 3-D printer media among other applications.     

Low Latency High Bandwidth Message Transfer Mechanisms for a Network Interface Plugged into a Memory Slot

The communication architecture of the DIMMnet-1 network interface based on MEMOnet is described. MEMOnet is a class of a network interface plugged into a memory slot. This paper proposes three message transfer mechanisms named atomic on-the-fly sending (AOTF), block on-the-fly sending (BOTF) and OTF receiving with selective address translation. The DIMMnet-1 prototype will have an ASIC named Martini, two banks of PC133 based SO-DIMM slots and an 8 Gbps full duplex optical link. The software overhead incurred to generate a message is only 1 CPU cycle and the estimated hardware delay is 105 ns using AOTF. The estimated hardware delay for receiving to on chip memory using OTF receiver is 90 ns. The estimated achievable sending bandwidth of DIMMnet-1 using BOTF is 984 MB/s which was observed in our experiments. This bandwidth is 7.4 times higher than the maximum bandwidth of PCI. This high performance is available even when simultaneous sending and receiving are executed on a cheap personal computer with DIMM slots. This paper also discribes the effects of BOTF for a PCI-based NIC.     

Easily assembled digital data acquisition system for the analytical ultracentrifuge

A system for the acquisition of digital data from the analytical ultracentrifuge which uses a commercially available data acquisition board, a standard IBM compatible personal computer (PC), and an interface circuit has been developed. The system uses the signal from the standard Beckman scanner. Preliminary analysis and data reduction are performed at the PC within minutes of data acquisition using simple commercially available software, and final data fitting is performed with a mainframe computer. Procedures are described which allow approach to equilibrium to be followed and attainment of equilibrium to be demonstrated. Data density of 200 points per millimeter column height (500 points per 100 μ1 of sample) allows the use of short columns and hence short run times. Only 2 min are required to collect a complete scan, which is recorded in a format suitable for direct analysis by standard spreadsheet software. This allows multiple sequential scans to be quickly recorded at equilibrium and averaged to reduce noise prior to analysis. The combination of characteristics allows molecular weight determinations to be performed relatively quickly with only a few micrograms of protein. The system is inexpensive and easy to assemble given the centrifuge and a PC.     

A protein secondary structure prediction scheme for the IBM PC and compatibles

A prediction scheme has been developed for the IBM PC and compatiblescontaining computer programs which make use of the protein secondarystructure prediction algorithms of Nagano (1977a,b), Gamieret al. (1978), Burgess et al. (1974), Chou and Fasman (1974a,b),him (1974) and Dufton and Hider (1977). The results of the individualprediction methods are combined as described by Hamodrakas etal. (1982) by the program PLOTPROG to produce joint predictionhistograms for a protein, for three types of secondary structure:-helix, ß-sheet and ß-turns. The schemerequires uniform input for the prediction programs, producedby any word processor, spreadsheet, editor or database programand produces uniform output on a printer, a graphics screenor a file. The scheme is independent of any additional softwareand runs under DOS 2.0 or later releases. Received on January 26, 1988; accepted on May 24, 1988     

A software tool for standardised non-destructive biomass estimation in short rotation forestry

Following an evaluation of the various methods available for non-destructive biomass estimation in short rotation forestry, a standardised procedure was defined and incorporated into a computer programme (BioEst). Special efforts were made to ensure that the system can be used by people who are unfamiliar with computers and mathematics. BioEst provides an interface between a calliper and a spreadsheet programme which was written in Microsoft Excel macro language. Therefore, it is simple to modify the programme and create personal protocols. BioEst can be run on a portable PC with Microsoft Excel for Windows. The computer continuously recalculates an estimate of the amount of biomass per hectare, as well as some summary statistics, when fed data on shoot diameter obtained by making row-section-wise measurements with a standard digital calliper. BioEst is available without cost from the author.     

PGAAS: a prokaryotic genome assembly assistant system

MOTIVATION: In order to accelerate the finishing phase of genome assembly, especially for the whole genome shotgun approach of prokaryotic species, we have developed a software package designated prokaryotic genome assembly assistant system (PGAAS). The approach upon which PGAAS is based is to confirm the order of contigs and fill gaps between contigs through peptide links obtained by searching each contig end with BLASTX against protein databases. RESULTS: We used the contig dataset of the cyanobacterium Synechococcus sp. strain PCC7002 (PCC7002), which was sequenced with six-fold coverage and assembled using the Phrap package. The subject database is the protein database of the cyanobacterium, Synechocystis sp. strain PCC6803 (PCC6803). We found more than 100 non-redundant peptide segments which can link at least 2 contigs. We tested one pair of linked contigs by sequencing and obtained satisfactory result. PGAAS provides a graphic user interface to show the bridge peptides and pier contigs. We integrated Primer3 into our package to design PCR primers at the adjacent ends of the pier contigs. AVAILABILITY: We tested PGAAS on a Linux (Redhat 6.2) PC machine. It is developed with free software (MySQL, PHP and Apache). The whole package is distributed freely and can be downloaded as UNIX compress file: ftp://ftp.cbi.pku.edu.cn/pub/software/unix/pgaas1.0.tar.gz. The package is being continually updated.     

Integration of a barcode reader with a commercial flow cytometer.

This report describes the application and installation of a barcode reader on a standard EPICS Elite flow cytometer. The barcode reader system eliminates keyboard entry of sample information on the cytometer. The system automates the transfer of sample information already present in our laboratory database to the cytometer at run time. The system uses a standard "off-the-shelf" bar code wand with a personal computer keyboard interface and requires no additional software at run time. No typing of sample information is required by the operator at any stage of normal sample operation at the cytometer. All operations are automatically coded into the cytometry software using the macro functions of the software. Tubes are inserted into the tube reader and sample information is transferred automatically into the cytometer. We have found that the system allows rapid and continuous operation of routine clinical and research samples. This automated data entry also reduces the possibility of data input errors.     

Involving undergraduates in the annotation and analysis of global gene expression studies: creation of a maize shoot apical meristem expression database

Through a multi-university and interdisciplinary project we have involved undergraduate biology and computer science research students in the functional annotation of maize genes and the analysis of their microarray expression patterns. We have created a database to house the results of our functional annotation of >4400 genes identified as being differentially regulated in the maize shoot apical meristem (SAM). This database is located at http://sam.truman.edu and is now available for public use. The undergraduate students involved in constructing this unique SAM database received hands-on training in an intellectually challenging environment, which has prepared them for graduate and professional careers in biological sciences. We describe our experiences with this project as a model for effective research-based teaching of undergraduate biology and computer science students, as well as for a rich professional development experience for faculty at predominantly undergraduate institutions.     

Developing a Hybrid Programmable Logic Controller Platform for a Flexible Manufacturing System

In this article, we present the design and implementation of a flexible manufacturing system (FMS) control platform based on a programmable logic controller (PLC) and a personal computer (PC)-based visual man-machine interface (MMI) and data acquisition (DAS) unit. The key aspect of an FMS is its flexibility to adapt to changes in a demanding process operation. The PLC provides feasible solutions to FMS applications, using PC-based MMI/DAS, whereby PLCs are optimized for executing rapid sequential control strategies. PCs running MMI/DAS front-ends make intuitive operation interfaces, full of powerful graphics and reporting tools. Information from the PC can be distributed through a company's local area network or web using client-server technologies. Currently, with the convergence of underlying microprocessor technology and software programming techniques, many users find that PLCs provide a cost-effective solution to real-time control in small- to medium-sized process plants, especially when combined with supervisory PCs using hybrid systems. The major work of this article demonstrates that PLCs are responsive to rapid and repetitious control tasks, using PCs that present the flow of information automation and accept operator instructions, thereby providing the user a tool to modify and monitor the process as the requirements change.     

A Simple Computer-aided Device for Monitoring Activity of Small Mammals and Insects

A simple computer-aided device was developed to record the activity of small animals. The device comprises of aktographs, opto-couplers, opto-amplifier units, a data acquisition unit (‘Activity Monitor’) and a Pentium processor based personal computer (PC) attached to an addition parallel printer port. The aktographs are devices which facilitate organisms to exhibit its natural activity. The aktographs for fruit flies, ants and mice are tubes with food supply and moisture, petri dishes adequately ventilated with arrangements for constant supply of water, sugar or honey solution, and cages attached with running wheels, respectively. Two mutually perpendicular beams of infra-red (IR) emission form a cross-hair detection system across the aktographs and an interruption to these beams creates an electrical signal (‘transition’) which is amplified using the opto-amplifier unit and sent to the activity monitor which consists of shift registers. The number of moments the IR beams are interrupted is taken as a measure of the amount of activity, based on the assumption that a more active animal would interrupt the IR beams more often compared to a less active one. Programs were written in C++, which facilitated data acquisition and graphical representation in terms of a daily plot of amount of activity as a function of time of the day, and actograms of daily activity were arranged chronologically one below the other. The activity patterns of individual animals (fruit fly, ants, and mice) were monitored using this device. Based on the performance and features of this device, we feel that with some improvement in the software this can substitute some of the existing activity recording devices, which are costly and not flexible.     

A Simple Computer-aided Device for Monitoring Activity of Small Mammals and Insects

A simple computer-aided device was developed to record the activity of small animals. The device comprises of aktographs, opto-couplers, opto-amplifier units, a data acquisition unit ('Activity Monitor') and a Pentium processor based personal computer (PC) attached to an addition parallel printer port. The aktographs are devices which facilitate organisms to exhibit its natural activity. The aktographs for fruit flies, ants and mice are tubes with food supply and moisture, petri dishes adequately ventilated with arrangements for constant supply of water, sugar or honey solution, and cages attached with running wheels, respectively. Two mutually perpendicular beams of infra-red (IR) emission form a cross-hair detection system across the aktographs and an interruption to these beams creates an electrical signal ('transition') which is amplified using the opto-amplifier unit and sent to the activity monitor which consists of shift registers. The number of moments the IR beams are interrupted is taken as a measure of the amount of activity, based on the assumption that a more active animal would interrupt the IR beams more often compared to a less active one. Programs were written in C++, which facilitated data acquisition and graphical representation in terms of a daily plot of amount of activity as a function of time of the day, and actograms of daily activity were arranged chronologically one below the other. The activity patterns of individual animals (fruit fly, ants, and mice) were monitored using this device. Based on the performance and features of this device, we feel that with some improvement in the software this can substitute some of the existing activity recording devices, which are costly and not flexible.     

Head Pilot: A new webcam-based Head Tracking System tested in permanently disabled patients

Persons with cerebral palsy (CP) need to modify their lifestyle in order to carry out daily activities. Assistive technology facilitates communication and improves the domestic environment and mobility. The STARNAV Company has developed a Head Tracking System, Head Pilot, which uses a robust algorithm that measures, in real-time, head motion from a webcam. Head Pilot aims to control any informatic and domotic interface controlling the pointer of a PC. This work aims to create an assistive technology that is easy to use once it is set up and used. The system offers an interface control, which allows individual users to adjust the system for their comfort. The system displays a toolbar allowing the patient to choose the velocity of the pointer and to choose from several different ways to validate a task. The objective of this study was to evaluate the performance of Head Pilot by using five computerized tests of validation. Seven participants with disabilities were compared to seven participants with no relevant medical history (control group). Two versions of the software were developed and displayed on a computer screen. The time to complete the tests were measured and compared to a control group. Before testing, the disabled persons had received an orthoptic assessment, a cognitive evaluation, and a cervical motor check. Head Pilot was validated for use by the majority of users with CP who were able to control a computer except for the subject with incomplete locked-in syndrome, who required an Eye Tracker System.     

PaperChase: a user-friendly program for searching the biomedical literature

PaperChase is a computer program which provides an efficient interface to the National Library of Medicine's MEDLINE database of references to the biomedical literature. The database includes references (citations) and abstracts compiled from Index Medicus, the International Nursing Index and the Index to Dental Literature. PaperChase may be accessed using any computer terminal or personal computer with modem. No special knowledge of computers or biomedical terms is necessary. Simple menus enable the novice to search the biomedical literature without training. A command language speeds searching for the experienced user. PaperChase does not require the user to know the database's indexing terminology, called Medical Subject Headings. Everyday language may be used and PaperChase will translate, or "map", the user's search term into the required Medical Subject Heading. PaperChase monitors a search in progress and suggests additional Medical Subject Headings which can be used to broaden or narrow a search. The searcher can order a full-text photocopy of any reference found in PaperChase. Support documentation and a subscriber newsletter are provided at no charge. Trained search specialists are available to offer assistance and to answer questions.     

BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster

BeoBLAST is an integrated software package that handles user requests and distributes BLAST and PSI-BLAST searches to nodes of a Beowulf cluster, thus providing a simple way to implement a scalable BLAST system on top of relatively inexpensive computer clusters. Additionally, BeoBLAST offers a number of novel search features through its web interface, including the ability to perform simultaneous searches of multiple databases with multiple queries, and the ability to start a search using the PSSM generated from a previous PSI-BLAST search on a different database. The underlying system can also handle automated querying for high throughput work. AVAILABILITY: Source code is available under the GNU public license at http://bioinformatics.fccc.edu/     

Plasmid map: a microcomputer program for display and storage of plasmid data

We describe a plasmid map program which runs on an IBM PC microcomputer and facilitates the drawing of circular plasmid maps. The user enters information from the keyboard in the form of restriction enzyme sites, genes and their locations, and other plasmid markers such as promoters, origins, or other sites. This information can then be stored in a file for future reference. The plasmid map can be displayed on the screen, printed on a dot-matrix printer, or plotted on a Hewlett Packard HP7475A plotter.     

AraCyc: a biochemical pathway database for Arabidopsis

AraCyc is a database containing biochemical pathways of Arabidopsis, developed at The Arabidopsis Information Resource (http://www.arabidopsis.org). The aim of AraCyc is to represent Arabidopsis metabolism as completely as possible with a user-friendly Web-based interface. It presently features more than 170 pathways that include information on compounds, intermediates, cofactors, reactions, genes, proteins, and protein subcellular locations. The database uses Pathway Tools software, which allows the users to visualize a bird's eye view of all pathways in the database down to the individual chemical structures of the compounds. The database was built using Pathway Tools' Pathologic module with MetaCyc, a collection of pathways from more than 150 species, as a reference database. This initial build was manually refined and annotated. More than 20 plant-specific pathways, including carotenoid, brassinosteroid, and gibberellin biosyntheses have been added from the literature. A list of more than 40 plant pathways will be added in the coming months. The quality of the initial, automatic build of the database was compared with the manually improved version, and with EcoCyc, an Escherichia coli database using the same software system that has been manually annotated for many years. In addition, a Perl interface, PerlCyc, was developed that allows programmers to access Pathway Tools databases from the popular Perl language. AraCyc is available at the tools section of The Arabidopsis Information Resource Web site (http://www.arabidopsis.org/tools/aracyc).     

Design of an automated temperature mapping system for ultrasound or microwave hyperthermia

An automated temperature mapping system was designed to accomplish the following goals: remote control mapping; a maximum position error of 0.5 mm; mapping simultaneously on several channels; real-time screen display on a dedicated computer; to be inexpensive; and have a simple patient interface and set up. A four channel, microstepper system was fabricated for less than $1000 and controlled by an IBM-AT computer. The system utilizes direct drive of Luxtron fibre-optic probes fed through thin flexible Teflon^® tubing which allows for patient movement. The driving and control software were written in the programming language “C”. Mapping parameters for each independent channel include start and stop positions and map increment. The software permits the user to automatically find the maximum temperature along a track in three passes of 2.0, 1.0 and 0.5 mm steps. The latter two passes take five or seven readings centred about the maximum of the previous pass. A high resolution monitor plots the temperatures in real time, overlaying the previous map in a new colour. A screen dump was written to drive a colour printer with the plot information. The computer evaluates each plot to safeguard against any shift in the maximum location. Visualization of orthogonal pullbacks provides rapid feedback and aids in the repositioning of superficial hyperthermia transducers. The time saved over the previous manual mapping methods easily justifies the additional set up time.