The BIONETt™™ Resource Description and Application Fom The BIONETtM Resource is a central computer facility serving the computational needs, for both research and communication, of the molecular biology community. The Resource is funded by a five year, cooperative agreement with the Biomedical Research Technol ogy Program, Division of Research Resources, National Institutes of Health. The IntelliGenetics Division of IntelliCorp, Palo Alto, California, will provide the computer facilities, core software, and support. Responsibility for overseeing the Resource rests with a National Advisory Committee (NAC), comprised of Drs. Joshua Lederberg (Chair, Rockefeller), Saul Amarel (Rutgers), Fotis Kafatos (Harvard), Allan Maxam (Harvard Medical School), Thomas Rindfleisch (Stanford), Richard Roberts (Cold Spring Harbor), and Charles Yanofsky (Stanford). Please read the following description of the BIONET Resource carefully. By signing the attached application form you will be agreeing to adhere to both the letter and the spirit of the guidelines described here. DESCRIPTION BIONET Goals The BIONET Resource has three goals: 1. To provide computational assistance in data analysis and problem solving for molecular biologists and researchers in related fields 2. To serve as a focus for development and sharing of new software tools 3. To promote collaboration and rapid sharing of information among a national community of scientists Hardware, Software, and Resource Envi ronment The computer hardware of the Resource includes: * An interactive, timesharing computer (Digital Equipment Corporation 2060) and associated peripheral equipment (tape drives, disks) * Telecommunication access to the computer, locally via dial-in, remotely via the nationwide Telenet network The computer software is divided into four categories: * The Core Library, consisting of nine programs from IntelliGenetics (see attached description), for manipulating and analyzing nucleic acid and protein sequence data, plus additional programs selected by the NAC * The Database Library, containing existing databases of nucleic acid and protein sequences, including GenBankt™, the European Molecular Biology Laboratory (EMBL) database, the National Biomedical Research Foundation (NBRF) library of protein sequences, and VectorBankt™ * The System and Programming Support Library, providing tools for program development, to include programming languages Fortran, C, Pascal, BASIC and MAINSAIL, and system utility programs (MLAB, for mathematical modeling, EMACS and TVEDIT for text editing, and SCRIBE for document preparation). Facilities for electronic mail and electronic bulletin boards will also be provided to foster rapid communication and collaboration. KERMIT will be available for file transfer to and from the Resource * The Contributed Library, for programs contributed and being developed by the BIONET community. Mature versions of such programs will be moved to the Core Library at the discretion of the NAC The Resource staff wil] provide this support to the BIONET community: * User consultation by telephone and on-line communication * Documentation of programs in the Core Library * Regional training sessions in use of the software * Assistance in moving programs into the Contributed and Core libraries Service and Collaborative Activities Class I Users: Most members of the BIONET community will be Class I users. These users will have access to the programs in the Core, Database, and Contributed Libraries, and to the electronic mail and bulletin board facilities. They will use these resources to support their current research, and to contribute infomation to the Resource community. Class II Users: Class II users will contribute programs to or collaborate in developing new programs for the BIONET Resource and will have access to all four categories (above) of system resources to aid in this effort. Criteria for Eligibility The NAC has set these criteria for eligibility: Class I--The BIONET Resource will admit, pro forma, researchers from acadenic and non-profit institutions in the U.S., who can demonstrate that they are supported by governmental, philanthropic, or unrestricted institutional funds and that their research can be assisted by the Resource facilities. The BIONET staff will consider on a case-by-case basis applications from investigators in foreign countries or from investigators funded from proprietary or restricted sources, and make recommendations to the NAC, which will] make final decisions on all access to the Resource. Class IIl--These users must meet the admission requirements for Class I access. In addition, they must indicate that they will participate in developing the Resource, by providing new programs to the BIONET community that help achieve the goals described above. Conditions and Restrictions The NAC will approve all access and will make the final judgment on applications that are questionable in nature, scope, or funding of research. Investigators outside of the U.S., who are accepted into the Resource, must pay for telecommunications to the BIONET computer. Access to BIONET will be approved through March 1, 1986, and will thereafter be subject to yearly renewal by reapplication. Standard DEC-2060 facilities for file protection will be available to protect the integrity of preliminary data and programs. Ownership of data and software developed on the Resource will be subject to the guidelines of the Principal Investigator's institution and granting agency, to which al]? questions on legal issues should be directed. However, such data and software will be in the public domain in that the Resource will have a non-exclusive right to use of this information by other BIONET investigators. All investigators granted BIONET access must provide brief annual summaries of research results. The summaries must be included in our annual report of Resource activities to the NIH. Investigators will have sufficient warning to prepare the summaries. Al] publications that involve use of the Resource must acknowledge the Resource by name and NIH grant number (1 U41 RRO1685-01). Investigators must send three (3) copies of these publications to the Resource Manager. Access to BIONET for Class I and I] users will be granted, on approval, to a Principal Investigator and designated members of his or her research group (see below). Each group will be allocated a fixed amount of disk storage space distributed among the PI and designated associates. We request that each PI limit access of his or her group to one login to BIONET at a time, j.e., two or more simultaneous logins are strongly discouraged during peak time (8:00 AM - 8:00 PM PST). Class II users will be granted larger amounts of disk space. BIONET will restrict the number of Class II users because of the anticipated heavy demands each will place on the facilities. Use of the Resource will be carefully monitored by the staff and the NAC. There will be no initial charge for access to the BIONET computer. The NAC and NIH may institute a fee-for-service in the future. Researchers will have sufficient warning of fees to include requests for additional funds in their research grant proposals. The BIONET Resource provides only a computer facility and associated services. It does not provide research equipment. The Resource has a smal] fund for fostering collaborations and will use this fund, when no other means are available, to support an effort that will advance the goals of the Resource. A limited fund is available to support the production and distribution of documentation. Approved applicants will receive, free of charge, introductory material on access to BIONET, use of electronic mail and bulletin boards, and brief descriptions of the use of each of the programs in the Core Library. A complete program reference manual is available, at cost, from BIONET for $35. Please indicate on the application form the number of copies desired. How to Apply Principal Investigators should complete (please type) and sign the attached application form. One application form provides access for a PI and all of the personnel within his or her research group, listed under "Additional Users". Please address the completed application and written inquiries for further infomation to this address: BIONET Applications c/o BIONET Manager IntelliGenetics, Inc. 124 University Avenue Palo Alto, CA 94301 GENED SEQ PEP MAP GEL SIZER QUEST IFIND CLONER Description of IntelliGenetics Programs in the Core Library an interactive sequence editor, to simplify entry of nucleic acid and protein sequence data an aid to the storage, retrieval and analysis of nucleic acid sequences an aid to the storage, retrieval and analysis of protein sequences a program to generate restriction enzyme maps from enzymatic digests used to manage large-scale DNA sequencing projects, including derivation of consensus sequences for calculation of molecular size of fragments from ge] mobility data a general purpose program for searching for complex patterns in nucleic acid and protein sequences determines the alignment and similarity of pairs of sequences a recombinant DNA simulation system that aids planning of experiments Page 1 of 5 APPLICATION FORM FOR CLASS I and II USERS The BIONET™™ Resource Principal Investigator (full name and title): Affiliation (Department, School and Institution): Mailing Address: Area code and phone number: Applying for Class I or Class II Use? Computers and terminals available (Specify only equipment that you would use to communicate with the Resource.): Computer experience (List computers and computer languages; specify none, casual use(C), moderate experience (M), or highly skilled (S).): Additional users (List al] BIONET users under your direction. For experience, specify none (N), casual (C), moderate (M), or skilled (S$). Highlight the primary contact person for your group if not yourself. The fixed disk space will be allocated among the names given, so please be judicious in selecting names): Computer Name Title Phone Experience Page 2 of 5 Application Form for Class I & II Users (continued) Please attach the following items to the application fom on as many pages as necessary. (Please type.) 1. Intended use of BIONET. Class I applicants should attach a short description labeled "Intended Use". "Intended Use" should include a Research Title of 80 characters or less, and a Research Abstract with a minimum of 3 lines and a maximum of 350 characters. Class II applicants, in addition, should include a description in detail of how their work will benefit the BIONET community. 2. Current grant support in area of intended use. Attach a sheet listing each federal grant by Principal Investigator, title, funding institution, grant number and duration of support and a brief (three to ten line) abstract of the research. If funding is from institutional or other unrestricted funds: (1) provide information on sources of funding sufficient for the NAC to determine if conditions for access have been met; and (2) provide the signature of an institutional official responsible for administering the grant. 3. Fill in the sheet labeled “APPENDIX TO INSTRUCTIONS - DRR SCIENTIFIC CLASSIFICATION." This information is required for reporting BIONET use to the NIH. Please select from "AXIS I" a maximum of four (4) codes that best describe your research area. Select from "AXIS II" a maximum of four (4) codes that further characterize your research. Circle or highlight the selected codes and return the sheet as part of your completed application. 4. BIONET will provide electronic bulletin boards on topics that you recommend. Please fill out and return the attached sheet on topics. 5. For Class II applicants, only. Current publications list in area of intended use (List only publications for the last two years.) Documentation Indicate the number of copies of BIONET reference manual desired Please enclose a check made payable to "BIONET Resource" for $35 a Copy. The BIONET Reference Manual may only be purchased by advance payment via check. Page 3 of 5 As Principal Investigator of this grant to use the BIONET Resource, I agree, by signing this application, to adhere to all conditions and restrictions for use of the BIONET Resource, as described in the attached document, "The BIONET(tm) Resource, Description and Application Form", and such further regulations as may be issued from time to time by the NIH or the NAC. The BIONET resource will not be used for any commercial purpose which is not specifically identified to and approved by the NAC. Any pertinent change in sponsorship, continuity of grant support, or use made of BIONET will be reported promptly to the BIONET Resource Manager. I have also furnished a copy of this application to the responsible administrative officer of my institution, namely: Name of official: I also assume full responsibility for all users listed on this application form and will monitor their compliance to the conditions and restrictions for access to the BIONET Resource. I will inform the BIONET Administrator, (electronic mail address MARTIN), by electronic mail, immediately about any changes in this group of users, j.e., departure of an existing user or addition of new staff qualified to use the Resource. I will inform new users of the above mentioned conditions and restrictions. Signature of Principal Investigator: Date: Mail the completed application to: BIONET Application c/o BIONET Resource Manager IntelliGenetics, Inc. 124 University Avenue Palo Alto, CA 94301 Incomplete applications will be returned to you for completion. Please send all inquiries about this application to the above address. Include your phone number and application date in all correspondence. Page 4 of 5 APPENDIX TO INSTRUCTIONS DRR SCIENTIFIC CLASSIFICATION AXIS I AXIS II Code RESOURCE MATERIAL/RESEARCH AREA Code RESEARCH AREAS Nos. (Maximum 4 Codes) Nos. (Maximum 4 Codes) 1 Animals 30 Aging a. Vertebrates, Mammal 32 Anesthesiology b. Vertebrates, Non-Mammal 34 Anthropology/’Ethnography c. Invertebrates 36 Behavioral Sci/Psychology/Social Sci 2 Biological/Chemical Compounds 38 Bioethics 3 Biomaterials 40 Communication Science 4 Celis & Subcellular Material 42 Computer Science 5 Human Subjects — 44 Congenital Defects or Malformations 6 Membrane/Tissue/Isolated Organ 46 Degenerative Disorders 7 Microorganisms 68 Device, Protheses, Intra/Extracorpore: a. Bacteria 50 Drug Studies b. Virus a. Toxic c. Orphan Drugs c. Parasites b. Other d. Other 52 Engineering/Bioengineering 8 Plants/Fungus 54 Environmental Sciences 9 Technology/Technique Development a. Toxic 10 Other CSPECIFY) b. Other 12 Clinical Trials 56 Epidemiology a. Multicenter b. Single Center 58 Genetics, Including Metabolic Errors rrr ee eee 60 Growth and Development ANATOMICAL SYSTEM/RESEARCH AREAS 62 Health Care Applications nr rn ee ne enn 64 Immunology and Allergy 13 Cardiovascular System 66 Infectious Diseases 14 Connective Tissue 68 Information Science 15 Endocrine System 70 Instrument Development 16 Gastrointestinal System 72 Mental Disorders/Psychiatry ae. Esophagus 74 Metabolism and Transport b. Gallbladder a. Carbohydrate c. Intestine b. Electrolyte & Water Balance d. Liver c. Enzymes e. Pancreas d. Gases 17 Hematological System e. Hormone 18 Integumentary System f. Lipid 19 Lymphatic and Recticulo- g- Nucleic Acid Endothelial System h. Protein & Amino Acid 20 Muscular System 76 Neoplasms/Oncology 21 Nervous System a. Benign 22 Oral/Dental b. Malignant 23 Reproductive System 78 Nutrition 24 Respiratory System 80 Radiology/Radiation Nuclear Medicine 25 Sensory System a. Ionizing (Xray, Nuclear Reactor) a. Ear b. Non-ionizing (Microwave, Radar) b. Eye 82 Rehabilitation c. Taste/Smeil/Touch 84 Statistics/Mathematics 26 Skeletal System 86 Surgery 27 Urinary System 88 Transplantation 26 Other CSPECIFY) 90 Trauma 92 Other (SPECIFY) Revised 1/31783 Page 5 of 5 ELECTRONIC COMMUNITIES All BIONET users will be required to participate in at least one User Community. These communities will be served by BIONET's Electronic Mail facility and Electronic Bulletin Boards, pemitting members of the individual communities to easily correspond with one another, exchanging research news and other items of mutual scientific interest. Please indicate which of the following communities you would like to participate in. Check AT LEAST ONE. 1. GENE EXPRESSION _ 2. PROTEIN ENGINEERING _ 3. DNA SEQUENCING __ 4. VECTOR CONSTRUCTION _ 5. METABOLIC REGULATION _ 6. DNA REPLICATION _ 7. DNA RECOMBINATION _ 8. DNA REPAIR _ 9. GENOMIC ORGANIZATION 10. IMMUNOLOGY 11. Other (Please Specify) COMMUNITY LEADERS Electronic Communities and Bulletin Boards will require organization and attention. Additionally, a very short summary of the activities of the community will be required describing the publications of individual community members, community research advances and contributions to the BIONET Resource as a whole. If you are interested in being a Community Leader, please indicate so bel ow: I am interested in being a Community Leader for the Electronic Community.