WO2005078578A1

WO2005078578A1 - Biological information unification device, biological information unification method, and biological information unification program

Info

Publication number: WO2005078578A1
Application number: PCT/JP2005/002055
Authority: WO
Inventors: Eiko Ohtsuka; Yutaka Tamura; Naoki Amano; Ryutaro Kurai
Original assignee: National Institute Of Advanced Industrial Science And Technology
Priority date: 2004-02-13
Filing date: 2005-02-10
Publication date: 2005-08-25
Also published as: JP2005228155A

Abstract

There are provided a biological information unification device, a biological information unification method, and a biological information unification program for automatically installing a biological analysis program on a network and using a plurality of biological analysis program in a unified environment. A biological information unification system (100) includes a biological information unification device (1), program providing servers (2a, 2b), and a service providing server (3). The biological information unification device (1) includes: interface means (21) for unifying the user environment; program processing means (23) for executing a biological analysis program installed; external service processing means (24) for utilizing the service of the service providing server (3); automatic installer means (25) for installing the biological analysis program provided by the program providing servers (2a, 2b); and program linkage processing means (26) for linking a plurality of biological analysis programs.

Description

Specification

Biological information integration device, biological information integration method, and biological information integration program

Technical field

The present invention relates to a biological information integration device for automatically installing a biological-related analysis program existing on a network, and utilizing a plurality of biological-related analysis programs in a unified environment. It relates to scientific information integration methods and biological information integration programs.

Background art

[0002] Bioinformatics, which applies computer-based information analysis techniques to biological problems, is currently developing rapidly. Various genome sequencing projects around the world are producing vast amounts of data on various organisms. Recently, many projects have been converted to a database and made available to the public. In particular, the analysis results of protein three-dimensional structures by mass spectrometers, NMR, and X-ray analyzers, which were awarded the 2003 Nobeli-Dani Prize, were published on the Web as a PDB database. In the research field related to, it is indispensable research data. Some researchers involved in life sciences, etc. are developing software related to life sciences in order to easily access and use these data via the Internet for further analysis. Some are. Specific examples are: 1) Modeller that predicts the three-dimensional structure of a protein when the structure is determined using the three-dimensional structure information of the protein registered in the PDB.

swiss-model, 2) procheck to determine the validity of the predicted structure of the protein by Modeller, etc., 3) BLAST to search for proteins with a structure similar to any amino acid sequence. In addition to the above, a number of programs have been produced, and books describing how to build and use these computer-based tools have been sold. (Cynthia Gibas, Per Jambeck) Written by Hiroshi Mizushima, Hiroshi Akashi, and translation without words, "Practical Bioinformatics: Computer Skills for Genomic Research," 1st Edition, Oraichi 'Japan, January 28, 2002, pp. 135-291 ;;). [0003] Some of these softwares are charged, but many are provided free of charge, and are available to anyone with a personal computer and Internet connection. However, these softwares have not been used effectively by many life science researchers, especially those engaged in experiments on cells and animals. The reason for this is that most of the software that is currently being published has a command line interface (hereinafter referred to as “CUI”) that runs on Unix (registered trademark) or Linux, and is available on Macintosh (registered trademark) and Windows (registered trademark). It is conceivable that a life science researcher using a graphical user interface (hereinafter referred to as “GUI”) of a trademark as a main component would be unwieldy. Another problem is that the data format required by each program is different for each program. For example, in the above procheck, if you obtain a PDB file, you only need to specify the options when calling the program. In Modeller, in addition to the PDB file which is a three-dimensional structure file, You must prepare two types of files: a file that describes the amino acid sequence of the protein you want to predict, and a simple script file that describes the structure prediction procedure. In this way, the trouble of having to learn how to use each program and the inconvenience of having to prepare a separate script for using the program are added, and many life science researchers use these software programs sufficiently. To use it for

Disclosure of the invention

[0004] Therefore, the present invention provides a biological information integration device for automatically downloading published life science-related software and the like, using a graphical interface, a unified operation feeling, and simple operation. And a biological information integration method and biological information integration program.

[0005] In view of the above problems, a first feature of the present invention is that (a) program information storage for storing program information including program location information, download information, and installation information of a biological-related analysis program to be installed. And a list of non-installed programs to be downloaded is created based on the download information in the (oral) program information storage unit, and the biological-related analysis programs on the uninstalled program list are downloaded based on the program location information. , Biological related analysis pro downloaded based on installation information Prompts the user to select an organism-related analysis program to be executed and (c) if a plurality of organism-related analysis programs are selected, is it possible to cooperate with multiple organism-related analysis programs? (2) input information, output information of the installed biological-related analysis program, and a plurality of interfaces determined to be operable based on the input information and output information. A program input / output information storage unit that stores the linkage information of the organism-related analysis programs and an execution scenario that determines the order of the multiple organism-related analysis programs to be executed based on (e) the linkage information. A program coordination processing unit that performs coordination processing between related analysis programs, and And summarized in that a biological information integration device and a program processing means for executing in succession a number of biologically relevant analysis program.

[0006] Further, a first feature of the present invention is that (g) the interface means presents an external service that requires an external request so that the external service can be selected, and when an external service is selected, the interface means is provided to an apparatus that provides the external service. An external service processing means for making a service request and obtaining a service execution result is further provided. (H) The program processing means includes a GUI program attached to the installed organism-related analysis program. The apparatus further includes a data format information storage unit that executes the organism-related analysis program by adding the prepared GUI program and stores data format information used by the (re) installed organism-related analysis program.

The program coordination processing means, when coordination between a plurality of organism-related analysis programs to be executed requires data format conversion, performs data conversion based on the data format information in the data format information storage unit. May be added.

[0007] A second feature of the present invention is that (a) storing program information including program location information, download information, and installation information of a biological-related analysis program to be installed in a program information storage unit; Mouth) The automatic installer creates an uninstalled program list to be downloaded based on the download information in the program information storage unit, and downloads the biological analysis program on the uninstalled program list based on the program location information. (C) installing the biological-related analysis program downloaded based on the installation information; Prompts the user to select an organism-related analysis program to perform, and when multiple organism-related analysis programs are selected, a step of determining whether or not a plurality of organism-related analysis programs can be executed in cooperation with each other. The program input / output information storage unit stores the input information and output information of the related analysis program, and the link information of a plurality of organism-related analysis programs that can be linked by the interface means created based on the input information and output information. Based on the step (e) and the cooperation information, the program cooperation processing means creates an execution scenario that determines the order of the plurality of organism-related analysis programs to be executed, and executes the cooperation processing between the plurality of organism-related analysis programs. Steps to be performed, and a plurality of organism-related analysis programs in which program processing means are linked in accordance with the execution scenario. And summarized in that continuously a biological information integration method and a step of executing.

The third feature of the present invention is that (a) a biological-related analysis program required for analysis is installed from an external device, and program location information, download information, and installation information of the biological-related analysis program to be installed on a computer that performs arithmetic processing. An instruction to store program information including information in the program information storage unit and a list of uninstalled programs to be downloaded are created based on the download information in the program information storage unit, and the uninstalled program list is created based on the program location information. An instruction to download the organism-related analysis program on the list and to install the downloaded organism-related analysis program on the basis of the installation information to the automatic installer means, and (c) selection of the organism-related analysis program to be executed To encourage When two or more object-related analysis programs are selected, an instruction that allows the interface means to determine whether multiple organism-related analysis programs can be executed in cooperation with each other, and (2) input information and output of the installed organism-related analysis programs An instruction to store in the program input / output information storage unit the link information of a plurality of organism-related analysis programs determined to be linkable by the interface means created based on the information, input information, and output information; Based on the above, the program coordination processing means creates an execution scenario that determines the order of the multiple organism-related analysis programs to be executed. An instruction to continuously execute a plurality of organism-related analysis programs cooperatively processed by the program processing means. Is a biological information integration program that executes Is the gist.

Brief Description of Drawings

FIG. 1 is a schematic diagram of a biological information integration system according to an embodiment of the present invention.

FIG. 2 is a structural diagram of a biological information integration device according to an embodiment of the present invention.

FIG. 3 is a data structure diagram of program input / output information.

FIG. 4 is a flowchart showing an overall operation of the biological information integration device.

FIG. 5 is a flowchart showing an operation of the automatic installer.

FIG. 6 is a flowchart showing an operation of executing a specific program.

FIG. 7 is a flowchart showing an operation of preparing for cooperation of a plurality of programs.

FIG. 8 is a flowchart showing an operation of coordinating and executing a plurality of programs.

FIG. 9 is a screen diagram when a specific program is executed.

FIG. 10 is a screen view when a plurality of programs are executed.

BEST MODE FOR CARRYING OUT THE INVENTION

Hereinafter, a biological information integration device, a biological information integration method, and a biological information integration program according to an embodiment of the present invention will be described. Note that the devices, techniques, and the like used in the embodiments of the present invention are merely examples, and the present invention is, of course, not limited to these.

[0011] (Biological Information Integration System)

The biological information integration system 100 according to the embodiment of the present invention automatically installs a biological-related analysis program existing on a network and uses the environment of a plurality of biological-related analysis programs in a unified manner. Things. For example, to predict the three-dimensional structure of one sequence, 1) homologous search of the sequence into the structural database (eg, Blast), 2) closest homologous !, sequence and alignment (eg, program) : ClustalW), 3) Cut out the part where the three-dimensional structure coordinates are projected, 4) Predict the three-dimensional structure by homology modeling (use example: Modeller), 5) Correct the completed three-dimensional structure as a protein structure, 6) It is necessary to perform a process such as checking of the three-dimensional structure (example of program used: Rasmol), etc., and using a different bio-related analysis program in each process. . Data transfer and data conversion in each process Etc. are automatically performed in the biological information integration system 100.

As shown in FIG. 1, the biological information integration system 100 includes a biological information integration device 1, program providing servers 2a and 2b, a service providing server 3, and the like. These devices are connected to a network such as the Internet. Connected at 4.

[0013] The program providing servers 2a and 2b provide programs for information biology research such as Blast, ClustalW, Modeller, Procheck, and Rasmol. The service providing server 3 provides services such as data search processing for information biology research.

The biological information integration device 1 includes an interface unit 21, a program processing unit 23, an external service processing unit 24, an automatic installer unit 25, a program cooperation processing unit 26, and the like.

[0015] The automatic installer means 25 automatically installs the organism-related analysis program provided by the program providing servers 2a and 2b on the external network. In the automatic installer means 25, a biological-related analysis program to be installed such as program location information and installation-related information is defined in advance. Based on this information, the program accesses the program providing servers 2a and 2b to execute the program. Is downloaded and installed in the biological information integration device 1. In addition, the download and installation information of the program, which is the premise of the program, is also defined in advance. As a result, all the biological-related analysis programs required at the start of using the biological information integration device 1 can be prepared.

[0016] The program cooperation processing means 26 connects a plurality of installed biological-related analysis programs when a plurality of programs are continuously operated, automatically exchanges data between the programs, and outputs a final result. Only to the user. If data conversion is required for data transfer between programs, data conversion processing is also performed.

[0017] The program processing means 23 executes data calculation processing using the installed biological-related analysis program.

[0018] The interface means 21 unifies the user environment when using a plurality of organism-related analysis programs. Provide a common interface integrated with users. In addition, for a biological analysis program that does not have a GUI, a GUI for the program in which the interface means 21 is prepared in advance is provided. This allows the biological functions that were running on the command line Realizes a graphical environment for a continuous analysis program. When the user starts the program, the prepared GUI or the GUI of the program itself is displayed to operate the program.

The external service processing means 24 uses the service provided by the external service providing server 3 via the interface means 21. Therefore, an interface is prepared for each of the program providing servers 2a and 2b. When a request is issued to each interface, the external service processing means 24 sends the request to the service providing server 3 and obtains the result.

[0020] In the biological information integration system 100, the operation of each means is performed through an integrated interface, so that the user is aware of its functional capabilities S installed program capabilities, whether it is an external service, or the like. Can be used without doing.

[0021] In addition, even if the output format of each biological-related analysis program is a different data format such as text, portable document format (PDF), postscript, etc., it is converted into one data format and a single output format is used. Output.

[0022] (Biological information integration device)

Hereinafter, each means of the biological information integration device 1 will be described in detail. As shown in FIG. 2, the biological information integration device 1 according to the embodiment of the present invention includes an input device 11, an output device 12, a communication control device 13, a main storage device 14, and a central processing unit (hereinafter referred to as “CP Uj”). 20) and an auxiliary storage device 15.

The auxiliary storage device 15 includes a program information storage unit 16, a program input / output information storage unit 17, a data format information storage unit 18, and the like.

[0024] The program information storage section 16 stores program location information, download information, and installation information for each living-related analysis program to be installed from the program providing servers 2a and 2b. The program location information indicates a URL address or the like from which the program can be downloaded, the download information indicates a list of programs or files that need to be downloaded by the machine that executes the biological information integration device 1, and the installation information indicates a list of the files. This refers to the directory name used when installing files, the shell script describing the installation method when downloading multiple files, and so on.

[0025] The program input / output information storage unit 17 stores a program for an output program as shown in FIG. Multiple programs as shown in Fig. 3 (c), such as program name, input file name and input file format of input program as shown in Fig. 3 (b), such as program name, output file name and output file format In this case, information such as the program name of the program to be executed first, the program name of the program to be executed next, and the correspondence between parameters are stored. In Figure 3, first run the program "Modeller", it is set to the data file to be output to pass as an input file to the next program "p _roc h _ec k".

[0026] The data format information storage unit 18 stores information on conversion processing when converting the data format. For example, from a PDB format that describes protein structural information, you may want the sequence information in the FASTA format. In this case, information in the PDB format → FASTA format and a program for performing this data conversion are registered.

The CPU 20 includes an interface unit 21, a program processing unit with a GUI 22, a program processing unit 23, an external service processing unit 24, an automatic installer unit 25, a program cooperation processing unit 26, a result output processing unit 27, and the like. RU The biological information integration device 1 operates when the CPU 20 appropriately executes these means (programs).

The interface unit 21 includes a common function unit 21a, a program GUI control unit 21b, a program GUI cooperation unit 21c, and the like. The common function means 21a is an interface commonly used by each program, and is used for many programs such as operations for disclosing and saving files, displaying and editing base sequences and amino acid sequences, and displaying three-dimensional structures of proteins and the like. Supports commonly used functions.

The program GUI control unit 21b is an interface that controls the GUI for each program downloaded from the program providing servers 2a and 2b or for each service of the external service providing server 3. The program GUI control means 21b activates a predetermined GUI when the user wants to use a specific program or service. The user is presented with a plurality of programs as a selectable menu and urges the user to select a program to use. When the user inputs a selection of a program to be used, the program GUI control unit 21b stores the information in the program input / output information storage unit 17.

[0030] The program GUI cooperation means 21c presents a combination of program cooperation to the user side, and can cooperate with a plurality of programs selected by the user in a specified order. It is determined whether or not. If linkage is possible, the selected information is transmitted to the program linkage processing means 26. If the coordination is not possible, a notification that the coordination is impossible is displayed.

[0031] The GUI-equipped program processing means 22 performs arithmetic processing of a program already having a GUI among a plurality of installed programs.

[0032] The program processing means 23 includes a program GUI means 23a and a program execution means 23b. The program GUI means 23a adds a prepared GUI to a program having no GUI among a plurality of installed programs. The program execution means 23b performs an arithmetic operation of the program to which the GUI is added by the program GUI means 23a.

[0033] The external service processing means 24 includes an external service GUI means 24a, an external service request means 24b, an external service result processing means 24c, and the like.

When receiving a service request from the user to the service providing server 3, the external service requesting unit 24 b sends the service request to the service providing server 3 via the network 4. The external service result processing means 24c acquires the result of the service transmitted by the service providing server 3, and performs a certain process. The external service GUI means 24a is a GUI used for transmitting and receiving data between the service providing servers 3.

[0035] The automatic installer means 25 includes an automatic download means 25a, a program installation means 25b, a license information acquisition means 25c, and the like. The automatic download unit 25a downloads a desired program in a preset order based on the program location information and the download information in the program information storage unit 16. When the download by the automatic download unit 25a is completed, the program installation unit 25b automatically performs the process of installing the program based on the installation information. For a program that requests the user for information such as license information, the license information obtaining means 25c prompts the user to input the license information and performs a license obtaining process.

[0036] The program cooperation processing means 26 includes a program input / output information management means 26a, a data conversion means 26b, a program cooperation means 26c, and the like. The program input / output information management means 26a updates the registration of the program input / output information shown in FIG. [0037] The program linking unit 26c links a plurality of programs that input and output data so that they can operate as a single program. This connection is made based on the description of the program input / output information obtained by the program input / output information management means 26a. Further, the program linking means 26c notifies the program GUI linking means 21c in the interface means 21 of a program combination which can be linked in advance. User power When multiple programs are requested to execute, the programs are executed in sequence, and when one program ends, the input information of the next program is automatically generated based on the execution results. If the data format needs to be converted, the data conversion means 26b performs a process of converting the data format into a data format that allows the programs to cooperate. For example, conversion processing of various data formats is performed, such as extracting only file sequence data in the PDB format or converting a three-character display format of amino acids into a one-character display format of amino acids. The data conversion means 26b acquires a combination for data conversion and a processing program thereof from the data format information in the data format information storage unit 18.

[0038] The result output processing means 27 converts the program execution results into various formats such as text format, postscript format, PDF format, and image format. Output to

The input device 11 refers to a device such as a keyboard and a mouse of the device itself. Also, it refers to an interface that receives input signals from external devices such as the program providing servers 2a and 2b. The output device 12 refers to a device such as a CRT monitor, a liquid crystal monitor, and a printer of the own device. Also, it refers to an interface that transmits output signals addressed to external devices. The communication control device 13 generates and controls a control signal for transmitting and receiving data via a network 4 such as a wireless, wired, or optical fiber. The main storage device 14 temporarily stores a program describing a processing procedure and data to be processed, and delivers machine instruction data of the program according to a request from the CPU 20. The data processed by the CPU 20 is written to the main storage device 14. The main storage device 14 and the CPU 20 are connected by an address bus, a data bus, control signals, and the like.

(Operation of Biological Information Integration Device)

Next, a series of operations performed by the biological information integration apparatus 1 with the program providing servers 2a and 2b and the service providing server 3 in the biological information integration system 100 will be described below with reference to FIG. [0041] The operations of the biological information integration device 1 can be roughly divided into 1) specific program processing, 2) processing of multiple programs, and 3) use of external services. Is determined and executed. Note that the numbers given to the steps indicate an example of the flow of the processing, and the order of the operations is not determined by this.

(A) First, when the biological information integration device 1 is executed, it is determined in step S100 whether or not this is the first operation. If it is the first time, in step S105, the automatic installer means 25 is started, and the necessary program for the biological information integration device 1 is automatically downloaded and installed. With this installation, all the programs necessary for the biological information integration device 1 are available. The automatic installer means 25 also starts when a program is additionally installed. The details of this operation will be described later.

(B) In step S110, the common function means 21a shown in FIG. 2 is provided on the output device 12 with common functions such as file operations and printing, common menus for executing a specific program, and executing a plurality of programs. Is displayed to prompt the user to input a desired program. When a specific program is selected by the user, the process proceeds to step S115, and when a plurality of programs are selected, the process proceeds to step S140, and it is necessary to request an external service providing server 3 among the programs. When a program is selected, the process proceeds to step S165.

(C) First, when a specific program is selected, in step S115, the common function means 21a prompts the user to select a specific program to be executed. The program execution screen is displayed as shown in Figure 9. The menu bar contains file (file input / output) items, edit (array edit) items, display (array and three-dimensional structure display) items, program selection items 31, and multiple execution items that are common functions in the integrated environment. , Screen (display of the specified screen) item, and help item. These items are commonly used in multiple programs.

[0045] In step S120, if the program selection item 31 is selected, the program GUI control unit 21b starts the installed program and the service providing server 3 that can be supported by the biological information integration apparatus 1. The list of external services available via It is displayed on the output device 12 as shown in FIG.

In step S125, when one of the programs is selected via the input device 11 as the neutral force of the program selection item 31, the GUI-equipped program processing means 22 or the program processing means 23 shown in FIG. 2 executes the program. Do. In step S130, the execution result is displayed on the output device 12. In step S135, it is determined whether or not to continue the program processing. If the program processing is to be executed again, the process returns to step S120. If not, the processing of the specific program is terminated.

(D) When a plurality of programs are selected, in step S140, the common function means 21a prompts the user to select a specific program to be executed. The execution screen of the program is displayed as shown in Figure 10.

[0048] In step S140, when multiple execution 45 of the menu bar in Fig. 10 is selected, the program GUI control means 21b in Fig. 2 starts the installed program and service provision that can be supported in the biological information integration device 1. A list of external services available via the server 3 is displayed in the possibility list 41 of FIG. 10, and the user is prompted to select a combination of programs to be executed. For example, if a program A → B is selected and then B → C is selected, the program is executed as A → B → C. Next, in step S150, a plurality of programs are continuously executed in the selected combination. The details of this operation will be described later.

In step S155, the execution result of the program is displayed on the output device 12. In step S160, whether or not to continue the program processing is selected. If the program processing is to be executed again, the process returns to step S140. If not, the continuous execution processing of the plurality of programs is terminated.

[0050] (e) In step S165, when a menu requiring the use of the external service is selected by the user, in step S170, the external service executed by the external service GUI means 24a of FIG. Display on 12. This may be displayed in FIG. 9 or FIG. 10, or another screen may be displayed.

In step S175, the external service request unit 24b requests the service providing server 3 of FIG. 1 to process the selected external service via the external service GUI unit 24a. To do. In step S185, the external service result processing means 24c receives the result of this service, and performs certain processing such as displaying the service result in step S190. Since this external service use operation uses the same method as the use of other programs on the screen, the user can use the external service and determine whether or not the user can use the installed program. Don't be conscious!

[0052] Finally, in step S195, whether or not to continue the program processing is selected. If the program processing is to be executed again, the process returns to step S170. If not, the processing of the external service use program is executed. To end.

[0053] (Operation of automatic installer)

Next, the operation of the automatic installer means 25 in step S105 will be described with reference to FIG.

(A) First, in step S 200, the automatic installer 25 checks the registration status of the program information to be installed with reference to the installation information in the program information recording unit 16. In step S205, a list of non-installed programs that does not exist in the machine that executes the biological information integration device 1 is created based on the result of this investigation.

(B) In step S210, the automatic download unit 25a acquires the location and download information of the program in the non-installed program list from the program location information and download information in the program information recording unit 16, and in step S215 Download the program. Further, in step S220, the installation information of the downloaded program is obtained from the program information storage unit 16.

(C) Since some programs require license information at the time of installation, it is determined in step S225 whether a license is required. If a license is required, in step S230, the license information obtaining means 25c prompts the user to input license information, and obtains the input license information. This license information acquisition can be performed at the time of installation of each program, or by first asking the user to input the information necessary for installation first, and then automatically installing the rest.

(D) Next, in step S235, the program installation means 25b Perform a stall. Finally, it is determined in step S240 whether there is still a program to be installed. If the installation is still to be performed, the process returns to step S210. If the installation is not to be performed, the automatic installation is terminated.

(Operation of Executing Specific Program)

Next, the operation of executing the specific program in step S125 will be described with reference to FIG.

(A) First, in step S310, it is determined whether or not the selected specific program has a unique GUI. If there is no unique GUI, in step S315, the program GUI unit 23a of the program processing unit 23 shown in FIG. 2 displays a GUI prepared for this program. For example, assume that a program for protein structure evaluation called “Procheck” is selected in program selection item 31 in FIG. At this time, since a program called Procheck does not originally have a GUI, the program GUI means 23a displays a GUI for Prpcheck. If the program has a unique GUI, the program is started as usual, and the unique GUI is displayed.

(B) In step S320, the user inputs and operates these GUIs, and the program execution means 23b executes the arithmetic processing of the program based on the input information. For example, the Procheck menu item 33 in FIG. 9 is used to designate or enter the PDB format file (the file format of the information of the three-dimensional structure of the protein) to be inspected and the resolution of the inspection, and execute the calculation based on the input values. The status during execution can be viewed from the execution status monitor column 34 in FIG. In step S325, each execution program passes the calculation result to the program processing means 23.

(C) In step S330, if the calculation results of each program are in different file formats, the result output processing means 27 in FIG. 2 converts these file formats into a unified file format, and proceeds to step S335. For example, the data is output to the output device 12 as shown in an execution result display screen field 32 in FIG.

[0062] For example, Procheck has the ability to output a file in postscript format. In FIG. 9, the result output processing means 27 converts the file to pdf format and displays it. With this unified file format, the user is conscious of various operations such as displaying the results on the screen and printing them for each program. Can be operated.

(Operation of Preparation for Cooperation of Multiple Programs)

Next, the operation for preparing for cooperation of a plurality of programs in step S145 will be described with reference to FIG.

(A) First, in step S400, the program GUI linking means 23a of FIG. 2 can be used via the installed programs that can be supported by the biological information integration device 1 and the service providing server 3. A list of relevant external services is displayed in the possibility list column 41 in FIG. This prompts the user to select a combination of programs to be executed. Further, the user is prompted to input or select detailed setting items in the menu column 42 of each program in FIG.

(B) In step S405, when the combination of the program to be executed and the detailed setting items selected by the user are acquired, the program input / output information management unit 26a outputs the first program and inputs the next program. Is associated. Specifically, as shown in Fig. 3, which of the output results of the first program is used as the input parameter of the next program is specified.

(C) At the time of this association, the data conversion means 26b may perform data conversion. For example, if the output is a PDB format, which is the format of structural information, and the input is a FASTA format, which is sequence information, only the sequence information is extracted from the PDB format and converted to the FASTA format.

(D) In step S415, the program input / output information management means 26a defines the combined program information and registers it in the program input / output information storage unit 17 as shown in FIG. 3 (c). Finally, in step S420, it is determined whether or not there is a program to be further connected. If there is still a program to be connected, the process returns to step S400. If there is no program to be connected, this process ends.

(Operation of Cooperation and Execution of Multiple Programs)

Next, the operation of linking and executing a plurality of programs in step S150 will be described with reference to FIG.

(A) First, in step S 510, the program cooperation processing means 26 acquires the combined program information from the program input / output information storage unit 17. In step S515 In other words, based on the acquired program information, create an execution scenario for multiple programs in which the execution order of the programs is specified. This execution scenario is displayed in the multiple execution menu column 43 of FIG. The program linking means 26c executes the program according to the execution scenario. The execution status monitor column 44 in FIG. 10 displays this execution status.

(B) After executing the program, it is determined in step S525 whether or not there is a program to be executed thereafter. If there is a program to be executed, the process proceeds to step S530, where the data conversion means 26b converts the output information, which is the execution result of the program, to the next program as input information based on the information in the data format information storage unit 18 I do. Step S5

At 35, the input information of the next program is created, and the process returns to step S520 to execute the next program based on this input information.

(C) When there is no program to be executed, the process proceeds to step S540, and the execution result data is delivered to the result output processing unit 27. The result output processing means 27 displays this on the output device 12.

Industrial applicability

According to the biological information integration device, the biological information integration method, and the biological information integration program of the present invention, free and openly available life science-related software and the like are automatically downloaded and a graphical interface is provided. Can be used with a unified operation feeling and simple operation.

In particular, life science researchers who are unfamiliar with computers can easily use life science related software.

[0074] The biological information integration device 1 according to the embodiment of the present invention can be used as an integrated environment that is not a mere interface. For example, linking with individual external programs

However, it can be made independent as a component, and can be supplemented for use by users for plug-ins of Web browsers.

[0075] It is also possible to develop a multifunctional editor that can properly process the amino acid sequence of the protein to be analyzed or the sequence of character strings constituting the DNA base sequence as data handled by the user. In addition, by providing a GUI to the command interface program, the query sequence and template PDB distribution in homologous modeling can be obtained. It is possible to add a function to compare columns or display different parts in different colors.

[0076] There are two types of life science-related software provided by CGI on the Web! And those distributed as binaries or source programs. It can link with Web and CGI so that it can be handled without discomfort.

[0077] Furthermore, in order to prevent the operating environment of each software from being different, the same platform is used for the four platforms of Linux, Unix (registered trademark) (IRIX), Windows (registered trademark), and Macintosh (registered trademark). Can be developed as software that gives a sense of operation

Claims

The scope of the claims

[1] A program information storage unit that stores program information including the program location information, download information, and installation information of the organism-related analysis program to be installed, and a program to be downloaded based on the download information in the program information storage unit. An installation program list is created, the biological-related analysis program on the non-installed program list is downloaded based on the program location information, and the biological-related analysis program downloaded based on the installation information is downloaded. Automatic installer means for installing

Interface means for prompting the selection of the organism-related analysis program to be executed, and when a plurality of the organism-related analysis programs are selected, determining whether a plurality of the organism-related analysis programs can be executed in cooperation with each other,

Input information and output information of the installed biological-related analysis program and link information of a plurality of the biological-related analysis programs that are determined to be linkable by the interface means created based on the input information and the output information. A program input / output information storage unit for storing

Program cooperation processing means for creating an execution scenario for determining the order of the plurality of organism-related analysis programs to be executed based on the cooperation information, and performing a cooperation process between the plurality of organism-related analysis programs;

A program processing means for continuously executing a plurality of the organism-related analysis programs linked in accordance with the execution scenario

A biological information integration device, comprising:

[2] The interface means presents an external service requiring an external request in a selectable manner,

2. The external service processing unit according to claim 1, further comprising: an external service processing unit that requests a service to an apparatus that provides the external service when the external service is selected, and obtains an execution result of the service. Biological information integration device.

[3] The program processing means may include a GUI program attached to the installed biological-related analysis program. 2. The biological information integration device according to claim 1, wherein the biological information analysis program is executed.

[4] a data format information storage unit for storing data format information used by the installed organism-related analysis program,

The program coordination processing means, when coordination processing among the plurality of organism-related analysis programs to be executed requires data format conversion, performs data conversion based on data format information in the data format information storage unit. The biological information integration device according to claim 1, wherein:

[5] a step of storing program information including the program location information, download information, and installation information of the organism-related analysis program to be installed in the program information storage unit;

Automatic installer means creates an uninstalled program list to be downloaded based on the download information in the program information storage unit, and downloads the organism-related analysis program on the uninstalled program list based on the program location information. Performing the download, and installing the biological-related analysis program downloaded based on the installation information;

Interface means for prompting selection of the organism-related analysis program to be executed, and when a plurality of organism-related analysis programs are selected, determining whether a plurality of organism-related analysis programs can be executed in cooperation with each other;

Input information and output information of the installed biological-related analysis program and link information of a plurality of the biological-related analysis programs that are determined to be linkable by the interface means created based on the input information and the output information. Storing in the program input / output information storage unit;

Based on the cooperation information, the program cooperation processing means creates an execution scenario that determines the order of the plurality of organism-related analysis programs to be executed, and performs a cooperation process between the plurality of organism-related analysis programs;

According to the execution scenario, a step in which the program processing means continuously executes the plurality of biologically related analysis programs which have been subjected to the cooperative processing. And a method for integrating biological information.

[6] The determining step includes selectively presenting an external service that requires an external request,

When the external service is selected, the external service processing means further includes a step of requesting a service to an apparatus that provides the external service and obtaining an execution result of the service. Item 6. The biological information integration method according to Item 5.

[7] The executing step is characterized in that a GUI program is attached to the installed organism-related analysis program, and in that case, the organism-related analysis program is executed by adding a prepared GUI program. 6. The biological information integration method according to claim 5, wherein

[8] The method further comprises storing data format information used by the installed biological-related analysis program in a data format information storage unit.

The step of performing the coordination process includes, when coordination between the plurality of biologically related analysis programs to be executed requires data format conversion, converting the data based on the data format information in the data format information storage unit. The biological information integration method according to claim 5, wherein the method is performed.

[9] Install a biological analysis program required for analysis from an external device and install it on a computer that performs arithmetic processing.

An instruction to store program information including program location information, download information, and installation information of the organism-related analysis program to be installed in a program information storage unit;

A non-installed program list to be downloaded is created based on the download information in the program information storage unit, and the organism-related analysis program on the uninstalled program list is downloaded based on the program location information. An instruction to cause an automatic installer to execute an installation of the organism-related analysis program downloaded based on the installation information;

The user is prompted to select the organism-related analysis program to be executed. When a plurality of organism-related analysis programs are selected, a plurality of the organism-related analysis programs can be executed in cooperation with each other. A command for causing the interface means to determine whether the

Input information and output information of the installed biological-related analysis program and link information of a plurality of the biological-related analysis programs that are determined to be linkable by the interface means created based on the input information and the output information. To store the program in the program input / output information storage unit;

Based on the cooperation information, an instruction for causing a program cooperation processing unit to create an execution scenario that determines the order of the plurality of organism-related analysis programs to be executed, and causing the plurality of organism-related analysis programs to perform a cooperation process;

An instruction for causing the program processing means to continuously execute the plurality of biologically related analysis programs in accordance with the execution scenario

And a biological information integration program characterized by being executed.

[10] The instruction to make the determination includes selectively presenting an external service that requires an external request,

The method according to claim 11, wherein when the external service is selected, the external service processing means further includes a command for requesting a device that provides the external service for a service and acquiring an execution result of the service. The biological information integration program according to 9.

[11] The instruction to be executed is such that a GUI program is attached to the installed organism-related analysis program, and in case of!, Na! /, A GUI program prepared in advance is added to execute the organism-related analysis program. The biological information integration program according to claim 9, wherein:

[12] An instruction for storing data format information used by the installed biological-related analysis program in a data format information storage unit is further provided.

The instruction for performing the coordination process is, if coordination between the plurality of biologically related analysis programs to be executed requires data format conversion, based on the data format information in the data format information storage unit. 10. The biological information integration program according to claim 9, wherein: