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Connecting to NCBI services

Multiple methods are used to connect to the NCBI servers

MacVector uses two basic methods to connect to the NCBI BLAST and Entrez servers: WWW and FIREWALL. In addition, configuration settings are possible for the HTTP proxy address and port, and a proxy server address.

The precise methods used depend on the version of MacVector. The following discussion summarizes the modes used by MacVector 7.2.x and 8.0 to connect to the NCBI servers. Refer to the following NCBI document for additional details:

Previous versions of MacVector may not be able to connect to the NCBI servers due to changes at NCBI. Contact your MacVector, Inc. sales representative if you wish to upgrade your MacVector license.

WWW Mode (Default)

1. MacVector connects to the NCBI dispatcher at http://www.ncbi.nlm.nih.gov:80/Service/dispd.cgi on port 80 and requests a session.

2. The NCBI dispatcher assigns a server and returns the server address, port, and a session ticket to MacVector. The ticket contains a connection point to the BLAST or Entrez server and verifiable connection data.

3. MacVector disconnects from the dispatcher and initiates a connection to the address and port contained in the ticket.

4. The Entrez or BLAST server accepts the connection and processes the request.

WWW Mode (HTTP proxy specified)

HTTP proxy is only used when the connection occurs using the HTTP protocol. Direct TCP pipes are not affected by this setting.

1. MacVector connects to the web proxy server which translates the port to 80 and forwards the request to the dispatcher service.

2. Subsequent behavior is identical to the WWW Mode (Default) once the server address, port, and ticket have been received via the proxy.

1. MacVector contacts the NCBI dispatcher at http://www.ncbi.nlm.nih.gov:80/Service/dispd.cgi with the service name and specific parameters.

2. A service is started on the dispatcher via the firewall daemon at NCBI which generates a ticket that is returned to MacVector. The ticket contains either of the following connection points:

3. MacVector disconnects from the dispatcher and initiates a connection to the address and port contained in the ticket.

4. The Entrez or BLAST server accepts the connection and processes the request.

Firewall Mode (Proxy server specified)

1. MacVector connects to the proxy server which translates the port to 80 and forwards the request to the dispatcher service.

2. A service is started on the dispatcher via the firewall daemon at NCBI which generates a ticket that is returned to MacVector. The ticket contains either of the following connection points:

3. Upon receiving the ticket information from the NCBI dispatcher, MacVector connects to a local proxy server on ports 5861, 5862, or 5863.

4. The local proxy server will forward connection to the appropriate address:port pair. That is, if MacVector was given connection point 130.14.29.112:5861, it will connect to the proxy at port 5861, and the proxy should forward this connection to 130.14.29.112:5861.

Note: There must always be a port-to-port correspondence on the proxy.

Your ncbi.cnf file, Internet Control Panel settings, and the firewall or proxy server at your institution can contribute to the ability of MacVector to communicate with the NCBI servers.

If you have a problem connecting to the NCBI servers using MacVector, it could be due to the use of a network address translation (NAT) router, proxy server, or firewall at your institution. These can impede your ability to use MacVector which communicates with the NCBI servers on specific ports that must be accessible from your site. In some cases, it is possible to work around the firewall with the cooperation of your local network manager.

Note: Versions of MacVector prior to version 7.2 may not be able to communicate with the NCBI Entrez and BLAST servers due to changes at NCBI. If you are using MacVector 7.1.x, you can upgrade to MacVector 7.2.3 by downloading and installing the MacVector 7.2.3 updater from the MacVector web page (www.macvector.com). If you are using an earlier version of MacVector, please contact your MacVector, Inc. sales representative and request an upgrade quotation.

The first thing to do is determine whether your institution does indeed use a NAT router, proxy server, or firewall. If either case is true, then use the following instructions to configure MacVector. The following discussion describes how to (1) configure your Mac, (2) modify your proxy server or firewall, and (3) troubleshoot your connection. Step 2 must be performed by your network administrator.

1. Client configuration

If you're using OS 9.x, MacVector will honor the Internet Control Panel Advanced settings as described in the MacVector User Guide Appendix A. In this case, we recommend using the Internet Control Panel and discarding the ncbi.cnf file if it's present (normally present in the System folder or the System Preferences folder). You must be configured as an Advanced User to do this. Click Edit | User Mode and select Advanced. Next, click on the Advanced tab and select Firewalls from the chooser on the left side of the window. Try setting the proxy and socks settings from that control panel using information provided by your firewall administrator.

If you're using OS X, you must use an ncbi.cnf file to force MacVector 7.2.x and MacVector 8 to work with your firewall. This text file looks like this:

***********************************

[NET_SERV]

SRV_CONN_MODE=FIREWALL

SRV_HTTP_PROXY_HOST=your.proxy.com

SRV_HTTP_PROXY_PORT=80

SRV_PROXY_TRANSPARENT=no

***********************************

The ncbi.cnf file must be saved to your Users / "username" / Library / Preferences folder on OS X, or to the OS 9 System Preferences folder if you're using this approach on OS 9.

You will need to quit and restart your application in order for the network-aware settings to take effect. If you are behind a firewall, it must be configured correctly to access NCBI services. Your network administrator may have done this already. If not, please have them read the firewall settings section below.

2. Firewall / proxy server configuration

If you use a proxy server or a firewall, it must be configured to allow MacVector to access NCBI services on the appropriate ports. Create a TCP mapping service to let the proxy listen to port 8080, for example, for MacVector's request and redirect it to the NCBI dispatcher on port 80 and ports 4444-4544. The settings are:

Accept connection on port 8080.

Enable default mapping to www.ncbi.nlm.nih.gov on port 80 and ports 4444-4544.

Outgoing connections must be allowed on port 80 because MacVector first attempts to connect to the NCBI web site (http://www.ncbi.nlm.nih.gov) on the standard http port (80).

After the initial connection to the web server occurs, a token is returned to MacVector with an address and port for the actual query. In order for this to work, the firewall must allow outgoing connections on the following:

If your firewall is not transparent, the firewall port number should be mapped to the same port number on the external host.

3. Troubleshooting

You can test whether the NCBI ports are accessible from your machine independently of MacVector by opening a TELNET session to the NCBI. This can be performed by opening the OS X Terminal application and typing the following command at the system prompt:

and entering a carriage return or line of arbitrary text in the telnet session. If everything is fine, your TELNET session will look as follows (the line "test" is your input here):

Repeat the TELNET procedure as described above using ports 5862 and 5863.

A successful connection to the NCBI server would mean that the firewall or proxy server is correctly configured. If you are unable to connect to the NCBI server, the following results will appear:

After establishing that a successful connection is possible, you could address any further communication problems between MacVector and the firewall or proxy servers by modifying the Network Control Panel (OS 9), or the ncbi.cnf file (OS X).

In some cases, requests on certain port ranges may be blocked by a node somewhere on the route between your IP address and the NCBI. This would prevent you from communicating with the NCBI even though your Mac, MacVector, and the firewall may be properly configured. A "traceroute" analysis by your network admin may be helpful in diagnosing this situation.

Additional information is available at the following NCBI web site:

To communicate with a live human body knowledgable in all technical aspects of MacVector and Assembler, please call or email:

support@macvector.com

(919) 303-7450

(866) 338-0222

support@macvector.com

+44 (0) 1223 410 552

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