1. A method for modulating microbiota comprising
(i) analyzing a biological interaction network within a superorganism which includes at least one microbial derived component, wherein a superorganism is an organism consisting of many organisms, and wherein a microbial derived component is a microbe, or a gene, protein, transcript, carbohydrate, lipid, or metabolite derived from a microbe,
(ii) selecting a node or edge in the network, wherein a node is a terminal point or an intersection point of a graphical representation of a network; and wherein an edge is a link between two nodes, and
(iii) providing modulators of the node or edge.
2. The method of claim 1, wherein the modulator is selected from the group consisting of a small molecule, a protein, a carbohydrate, a lipid, a phage, a prebiotic, a probiotic, and a commensal organism, and combinations thereof.
3. The method of claim 1, wherein analyzing comprises the step of building a model of a biological interaction network using a method selected from the group consisting of a probabilistic bayesian network model, linear algebraic equations, partial least squares, Principle component analysis, Boolean models, and Clustering models.
4. The method of claim 1, wherein the network is selected from the group consisting of a bacterial interaction network, a bacterial-host interaction network, a whole-organism level interaction network, a biochemical interaction network, and a signaling network.
5. The method of claim 1, wherein the node is selected from the group consisting of a bacterial cell, a bacterial species, a bacterial protein, a bacterial enzyme, and a bacterial metabolite, wherein a node is a terminal point or an intersection point of a graphical representation of a network.
6. The method of claim 1, wherein the node is selected from the group consisting of a host cell, a host protein, a host enzyme, and a host metabolite, wherein a node is a terminal point or an intersection point of a graphical representation of a network.
7. The method of claim 1, wherein the edge is selected from the group consisting of a catalytic transformation, a complex formation, a signal transfer, regulation by a protein-protein interaction, a protein phosphorylation event, regulation of an enzymatic activity, and production of a secondary messenger, wherein an edge is a link between two nodes.
8. The method of claim 1, wherein the node or edge is selected based on a network parameter indicating the highest ranked node or edge according to a measure of relative prevalence, connectivity, evolutionary similarity, density, centrality, clustering coefficient, structural equivalence, and path length, wherein relative prevalence is the number of occurrences of a node divided by the total number of occurrences of all other nodes in a network; wherein connectivity is a measure of the number of edge connections of a node to the rest of nodes in the network; wherein evolutionary similarity is a measure of the degree of shared ancestry between two or more nodes; wherein density is the proportion of connections in a network relative to the total number possible connections; wherein centrality is a measure of the relative importance of a node or edge in the network based on one of four measures comprising degree centrality (the number of links incident upon a node), betweenness (the number of times a given node appears in shortest paths between other nodes), closeness (the distance between two nodes) and eigenvector centrality (the principal eigenvector of the adjacency matrix of a network); wherein the clustering coefficient is a measure of the likelihood that two nodes connected to a given node are also connected themselves; wherein structural equivalence is a measure of the extent to which nodes have a common set of connections to other nodes in the system; and wherein path length measures the distances between pairs of nodes in the network, with shorter distances being assigned a higher ranking.
9. The method of claim 1, wherein the network parameter is a measure of covariance.
10. A method for developing diagnostics for the determination of a physiological state comprising
(i) analyzing a biological interaction network within a superorganism which includes at least one microbial derived component,
(ii) selecting a node or edge in the network based on one or more network parameters, and
(iii) developing a diagnostic to measure the node.
11. The method of claim 10, comprising obtaining a sample from the group consisting of aurin, fecal, plasma, blood, saliva, sputum, CSF, and biopsy based test sample, for analysis.
The claims below are in addition to those above.
All refrences to claim(s) which appear below refer to the numbering after this setence.
1. A business practice management system, comprising:
a client contact management workflow including multiple stages of interaction between users of the system and clients of a business practice, including conditions for moving from one stage to another, said client contact management workflow defining interactions between the users of the system, the clients of the business practice, and information relating to the assets of the business practice, including tasks, events, forms, and conditions defined within multiple stages of the client contact management workflow;
a global business practice management workflow defining interactions between users of the system and one or more of the categories of the assets of the business practice independently of client contact stages, including tasks, events, forms, and conditions within the global workflow; and
one or more user interfaces that use the client contact management workflow and the global contact management workflow to interactively direct the users of the system in managing the assets of the business practice, wherein the tasks, events, forms, and conditions are adapted to direct the users in managing multiple categories of assets of the business, including employees, client accounts, inventory, and records.
2. The system of claim 1, further comprising one or more datastores for one or more categories of the information relating to one or more categories of the assets of the business practice.
3. The system of claim 1, further comprising business practice rules for managing one or more categories of the assets of the business practice, including tasks, events, forms, and conditions for interacting with the information relating to the assets.
4. The system of claim 1, further comprising an inventory management module that allows the users of the system to record amounts of items in inventory by scanning the items in and out of inventory using a bar code scanner.
5. The system of claim 1, further comprising an inventory management module that is integrated with said global business practice management workflow to direct users of the system in ordering more inventory based on the amounts of inventory and one or more inventory amount thresholds.
6. The system of claim 1, further comprising an inventory management module that is integrated with said client contact management workflow to reserve of an amount of an item for scheduled use in fulfilling needs of a client, and prevents users from removing the item from inventory based on the amount, the reservation, and a conflict with the scheduled use of the item.
7. The system of claim 1, further comprising a reporting module that allows users of the system to make and store records relating to one or more of goods supplied to clients or services rendered to clients, and to access the records.
8. The system of claim 1, further comprising a reporting module that is integrated with said client contact management workflow to direct users of the system to generate reports.
9. The system of claim 1, further comprising a payroll module that manages payment of employees of the business practice by automatically recording access of the system by employee users and calculating time worked by employees according to times of access.
10. The system of claim 1, further comprising an accounting module connected to an inventory management module that allows the users of the system to add items to inventory and remove items from inventory, wherein said accounting module and said inventory management module are configured to perform an automated bookkeeping function based on at least one of addition of items to inventory or removal of items from inventory.
11. The system of claim 10, wherein said inventory management module allows the users to add and remove items by scanning the items in and out of inventory using a bar code scanner, and the automated bookkeeping function is implemented to ensure that an entry is made in accounting books that debits an inventory asset account and credits an inventory expense account when inventory is scanned out, thus automatically expensing the inventory.
12. The system of claim 10, further comprising a payroll module, and a billing module, wherein the said contact management module, said payroll module, and said billing module are connected to said accounting module and configured to accomplish the automated bookkeeping functions based on actions of staff, payment of staff, and billing of one or more of clients and other responsible parties.
13. The system of claim 1, further comprising an accounting module integrated with said global business practice management workflow to allow users of the system to pay suppliers of inventory of the business practice.
14. The system of claim 1, further comprising an accounting module integrated with said client contact management workflow to allow users of the system to view and modify client account statuses, including invoicing clients of the business practice and marking client accounts as paid.
15. The system of claim 1, further comprising a billing module integrated with said client contact management workflow to allows users of the system to automatically generate bills based on one or more of goods and services rendered to a client of the business practice.
16. The system of claim 15, wherein said billing module is adapted to recommend specific billing codes based on procedures being performed.
17. A method of manufacturing a business practice management system, comprising:
defining a client contact management workflow including multiple stages of interaction between users of the system and clients of a business practice, including conditions for moving from one stage to another;
defining interactions between the users of the system, the clients of the business practice, and information relating to the assets of the business practice, including defining tasks, events, forms, and conditions within multiple stages of the client contact management workflow; and
defining one or more user interfaces that use the client contact management workflow to interactively direct the users of the system in managing the assets of the business practice, wherein the tasks, events, forms, and conditions are adapted to direct the users in managing multiple categories of assets of the business, including employees, client accounts, inventory, and records.
18. The method of claim 17, further comprising defining interactions between users of the system and one or more of the categories of assets of the business practice within a global business practice management workflow independently of client contact stages, including defining tasks, events, forms, and conditions within the global workflow.
19. The method of claim 18, further comprising defining one or more user interfaces that use the client contact management workflow and the global business practice management workflow to interactively direct the users of the system in managing the assets of the business practice.
20. The method of claim 17, further comprising defining one or more datastores for one or more categories of the information relating to one or more categories of the assets of the business practice.
21. The method of claim 17, further comprising defining business practice rules for managing one or more categories of the assets of the business practice, including defining tasks, events, forms, and conditions for interacting with the information relating to the assets.
22. The method of claim 17, wherein the tasks, events, forms, and conditions are defined within multiple stages of the client contact management workflow, and are adapted to direct the users of the system to manage employees, client accounts, inventory, and records of the business practice.
23. The method of claim 17, further comprising defining an inventory management module that allows the users of the system to record amounts of items in inventory by scanning the items in and out using a bar code scanner, directs users of the system in ordering more inventory based on the amounts, allows users to make a reservation of an amount of an item for scheduled use, and prevents users from successfully scanning out the item based on the amount, the reservation, and a conflict with the scheduled use of the item.
24. The method of claim 17, further comprising defining a reporting module that allows users of the system to make and store records relating to one or more of goods supplied to clients or services rendered to clients, and to access the records.
25. The method of claim 17, further comprising defining a payroll and accounting module that manages payment of employees of the business practice by automatically recording access of the system by the users, allows users of the system to place orders for inventory of the business practice, and records and communicates client account statuses.
26. The method of claim 17, further comprising providing a billing module that allows users of the system to automatically generate bills based on one or more of goods and services rendered to a client of the business practice.
27. An online business practice manager generation system, comprising:
a workspace provided to a subscribing user over a communications system;
a plurality of business practice management system definition services discoverable by said subscribing user employing said workspace,
wherein said services are operable to define workflows, business asset classes, user classes, and business rules processes within said workspace according to interaction with said subscribing user.
28. The system of claim 27, further comprising a user interface definition and editing service operable to allow the user to define one or more user interfaces.
29. The system of claim 28, wherein said user interface definition and edition service is operable to allow the user to select and edit a plurality of user interface templates authored to fulfill the needs of a variety of business practices.
30. The system of claim 27, further comprising a user class definition and editing service operable to allow the user to define one or more user classes.
31. The system of claim 30, wherein said user class definition and editing service is operable to allow the user to select and edit a plurality of user class templates authored to fulfill the needs of a variety of business practices.
32. The system of claim 27, further comprising a business assets information database definition and editing service operable to allow the user to define one or more asset information databases.
33. The system of claim 32, wherein said business assets information database definition and editing service is operable to allow the user to select and edit a plurality of database templates authored to fulfill the needs of a variety of business practices.
34. The system of claim 27, further comprising a business rules process management module definition and editing service operable to allow a user to define one or more business rules processes.
35. The system of claim 34, wherein said business rules process management module definition and editing service is operable to allow the user to select and edit a plurality of business rules process management module templates authored to fulfill the needs of a variety of business practices.
36. The system of claim 27, further comprising a workflow management module definition and editing service operable to allow a user to define one or more workflow management modules.
37. The system of claim 36, wherein said workflow management module definition and editing service is operable to allow the user to select and edit a plurality of workflow management module templates authored to fulfill the needs of a variety of business practices.
38. The system of claim 27, further comprising a workflow definition and editing service operable to allow the user to define one or more workflows.
39. The system of claim 28, wherein said workflow definition and editing service is operable to allow the user to select and edit a plurality of workflow templates authored to fulfill the needs of a variety of business practices.
40. A client contact management workflow software system, comprising:
a plurality of linearly ordered client contact workflow stages, wherein each stage is composed of required tasks, events, forms, and conditions, including conditions for stage completion, said stages including:
(a) an inquiry stage directing employees to collect and update information about a client;
(b) an appointment stage following completion of said inquiry stage, said appointment stage indicating that employees have scheduled an appointment for the client to meet with staff for a consultation; and
(c) a consultation stage following completion of said appointment stage, said consultation stage generating a consultation task for the staff based on the appointment, and recording information provided by the staff about results of the consultation.
41. The system of claim 40, further comprising:
(d) one or more procedures stages following completion of said consultation stage, one or more of said procedures stages signifying that at least one procedure has been booked, reserving inventory allocated for performing the one or more booked procedures, generating a bill for goods and services received by the client, directing the employees to invoice the client for the goods and services, generating one or more procedure tasks to be performed by the staff, and recording information provided by the staff about results of one or more of the procedures following completion thereof.
42. The system of claim 41, wherein said procedures stages are operable to direct employees to schedule a follow up for the client to meet with the staff following the procedure, the system further comprising:
(e) a follow up stage following completion of said procedures stage, said follow up stage generating a follow up task to be performed by the staff based on the scheduling of the follow up, and recording information provided by the staff about results of the follow up.
43. The system of claim 41, wherein said procedures stages further directs employees to remove items from inventory based on booked procedures.
44. The system of claim 41, wherein said procedures stages include two sequential stages, wherein a first stage is signifies that an appointment for a procedure has been booked and triggers tasks, events, and conditions that must be satisfied before a second of the stages, which triggers all of the tasks, events, and conditions that must be completed on a day of the procedure.
45. The system of claim 40, further comprising a global business practice management workflow directing employees to order items when a number of the items in inventory falls below a predetermined threshold.
46. The system of claim 40, further comprising a global business practice management workflow directing employees to enter items into inventory using a bar code scanner.
47. A method of providing online business practice management system, comprising:
providing online business practice management resources and services to users, including an online workspace via which users interact with business practice assets information;
providing business practice rules process modules for interacting with one or more categories of the business practice assets information;
providing a client contact management workflow including multiple stages for interaction between clients, the users, and the business practice assets information;
providing user interfaces integrated with the client contact management workflow to accomplish management of assets of the business practice by directing the users in interacting with the clients and the business practice assets information.
48. The method of claim 47, further comprising:
providing a global business practice management workflow for interaction between the users and the business practice assets information independently of client contact stages; and
providing user interfaces integrated with the global business practice management workflow to accomplish management of assets of the business practice by directing the users in interacting with the business practice assets information.
49. The method of claim 47, further comprising managing business practice assets including employees, client accounts, records, and inventory.
50. The method of claim 47, further comprising allowing users at the business practice to scan items in and out of inventory using a bar code scanner.
51. The method of claim 47, further comprising reserving items of inventory for scheduled services to clients and preventing removal of the items from inventory for other purposes.
52. The method of claim 47, further comprising generating a client invoice based on goods and services received by the client and directing employees to invoice the client.
53. A method of operation for an anatomical notation system, comprising:
presenting a user with a display of a plurality of icons representing selectable anatomical systems in the form of a dynamically rendered illustration of a human body;
varying display properties of selectable anatomical systems based on notes recorded in association with the selectable anatomical systems;
detecting user selection of one of the selectable anatomical systems;
adjusting the display to render the anatomical system selected by the user;
allowing the user to select a portion of a rendered anatomical system;
adjusting the display to enlarge display of the portion selected by the user, if any;
displaying notes recorded for the rendered anatomical system, if any;
displaying predetermined, selectable diagnoses for the rendered anatomical system;
accepting user specification of one or more notes and diagnoses associated therewith; and
recording user-specified notes and diagnoses in association with the anatomical system.
54. A medical information management system, comprising:
a datastore storing medical records including lab results and medical images;
a medical information management module adapted to access, retrieve, and store medical records, including lab results and medical images, in said datastore by employing a proprietary language; and
a translator module that allows multiple Electronic Medical Record (EMR) systems to speak to said medical information management module and to use that module as a means to communicate with each other, wherein said translator module is adapted to be connected between said medical information management module and the EMR systems, and to translate the languages that those EMR systems speak into the proprietary language and vice versa.
55. The system of claim 54, wherein a messaging language that can be understood by said translator module is Health Level 7 (HL7).
56. The system of claim 54, wherein a messaging language that can be understood by said translator module is the DICOM standard that has been created for medical images.
57. The system of claim 56, wherein said translator module is adapted to accept messages and store data in said database, and to accept requests for data and send data out to a requesting EMR application.