Install lrzsz before starting:

$ apt-get install lrzsz

I had some trouble using minicom (I didn't understand the instructions properly) so I've made a step-by-step guide - hopefully it saves someone else the troubles I had.

You can update Soekris Bios (any model) with Minicom and few steps. Before starting, download the latest available bios from soekris.com and save it in your home directory (minicom's file manager is a bit painful to browse around too much with - having the bin file in your home directory saves the hassle). Also, check if Minicom settings for serial ports (ctrl a+z and O on Minicom) match this:

Serial Device : /dev/ttyS0  (for first serial port on a PC - if you have a USB-2-serial converter it is usually called /dev/ttyUSB0))
Lockfile Location : /var/lock
Bps/Par/Bits : 19200 8N1
Hardware Flow Control : No
Software Flow Control : No

Here's what I did to update BIOS, step by step (everything after # is a comment, after > is what you type to the comBIOS monitor)

$ sudo minicom   # you probably need root privileges to get exclusive access to the serial port
Welcome to minicom 2.2

 OPTIONS: I18n
 Compiled on Apr 27 2007, 15:50:20.
 Port /dev/ttyS0

              Press CTRL-A Z for help on special keys

# turn on the Soekris board, and it starts the comBIOS (I have snipped some extra lines from the output)

POST: 012345689bcefghips1234ajklnopqr,,,tvwxy
comBIOS ver. 1.32i 20071005  Copyright (C) 2000-2007 Soekris Engineering.
net5501
0512 Mbyte Memory                        CPU Geode LX 500 Mhz
Pri Mas  SanDisk SDCFH-1024              LBA Xlt 993-32-63  1001 Mbyte

4 Seconds to automatic boot.   Press Ctrl-P for entering Monitor.

# here I hit Ctrl-P

comBIOS Monitor.   Press ? for help.

> download -

Start sending file using XMODEM/CRC protocol.

# Hit Ctrl-a, then z (presents the minicom menu) then s (for "Send file")
# this opens a text-mode dialog-box like this:

      +-[Upload]--+
      | zmodem    |
      | ymodem    |
      | xmodem    |
      | kermit    |
      | ascii     |
      +-----------+

# arrow-down to xmodem and hit Enter
# this will present a text-mode dialog to choose the file:

+------------------------[Select a file for upload]-------------------------+
|Directory: /home/fnerk                                                     |
| [.ssh]                                                                    |
| [Desktop]                                                                 |
| b5501_132i.bin                                                            |
| b5501_133.bin                                                             |
|              ( Escape to exit, Space to tag )                             |
+---------------------------------------------------------------------------+
              [Goto]  [Prev]  [Show]   [Tag]  [Untag] [Okay]

# arrow-down to the file you want, hit space-bar to select it, then hit Enter
# this will show another dialog to display transfer progress

        +-----------[xmodem upload - Press CTRL-C to quit]------------+
        |Xmodem sectors/kbytes sent:   0/ 0kRetry 0: NAK on sector    |
        |Retry 0: NAK on sector                                       |
        |Retry 0: NAK on sector                                       |
        |Retry 0: NAK on sector                                       |
        |Retry 0: NAK on sector                                       |
        |Retry 0: NAK on sector                                       |
        |Xmodem sectors/kbytes sent: 780/97k                          |
        +-------------------------------------------------------------+

# when the transfer is complete, it tells you so:

        +-----------[xmodem upload - Press CTRL-C to quit]------------+
        |Retry 0: NAK on sector                                       |
        |Retry 0: NAK on sector                                       |
        |Bytes Sent: 100352   BPS:1864                                |
        |                                                             |
        |Transfer complete                                            |
        |                                                             |
        | READY: press any key to continue...                         |
        +-------------------------------------------------------------+

# Note:  you are unable to transfer the file, change your Soekris serial speed to 9600. 

# hit enter, which will return you to the comBIOS prompt, and type flashupdate

> flashupdate
Updating BIOS Flash ,,,,,,,,,,,,,,,,,,,,,,,,,,,,..,,,,.... Done.

# and now reboot
> reboot

# and watch as your Soekris reboots with new BIOS:

comBIOS ver. 1.33  20070103  Copyright (C) 2000-2007 Soekris Engineering.

If minicom report errors during transfer, you can try this:

in minicom:

> download   

in another term, run the transfer command:

sx -X /tmp/b5501_133.bin > /dev/ttyS0 < /dev/ttyS0

Source: http://wiki.soekris.info/Updating_Bios