Use a loop to draw an axis using line();

 // This will draw a set of X axis
 pushMatrix();
 translate(0, y_min, z_min);
 float x_step = (x_max-x_min)/(number_of_grid_lines-1);
 float y_step = (y_max-y_min)/(number_of_grid_lines-1);
 float z_step = (z_max-z_min)/(number_of_grid_lines-1);
 for(int i=0; i<number_of_grid_lines; i++)
 {
   pushMatrix();
   for(int j=0; j<number_of_grid_lines; j++)
   {
     line(x_min, 0, 0, x_max, 0, 0);
     translate(0, y_step, 0);
   }
   popMatrix();
   translate(0, 0, z_step);
 }
 popMatrix();  


The above draws a set of x-axis ... modify accordingly to make the y and the z. (its also very rudimentary, with no auto-scaling or major/minor grid lines). As for drawing a sphere at a spot, simply translate to that point and make a sphere for each of your data points:

pushMatrix();
translate(point_x, point_y, point_z);
sphere(radius);
popMatrix();